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,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384],With:[3,4,7,13,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382],__future__:13,__main__:13,__name__:13,_combine_spec_dictionari:1,_descript:13,_dir:383,_famili:13,_file:383,_last_update_d:13,_series_matrix:[13,384],_stat:384,_statu:13,_submission_d:13,_summari:13,_titl:13,_type:13,_web_link:13,aa_:12,abil:[7,13,14,387],abl:[4,10,11,12,13,14,18,19,384],about:[0,1,4,7,11,12,13,14,16,18,19,382,386],abov:[4,5,10,13,14,15,16,18,384,386],absenc:13,acc:[13,14],accept:[13,16],access:[0,2,3,4,8,10,11,12,13,16,17,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,386],accord:[5,12,32,35,125,128,215,218,298,301],account:[3,6,7],accur:[3,8],accuraci:7,across:[12,15,104,194,280,365],act:[7,13],activ:[7,8,9,10,14,15,18,19,383,385,386],actual:[13,16,17,18],adar:[96,186,273,357],add:[1,3,4,5,6,7,8,10,11,12,13,14,17,19,382,386],add_argu:13,add_argument_group:13,added:[1,3,4,5,6,7,8,10,11,12,13,14,18,64,65,78,79,80,156,157,167,168,169,244,245,255,256,257,328,329,337,338,339,384,386],adding:[4,7,13,18,386],addit:[4,7,13,14,382,384,386],addition:[5,11,13,14,18,382,384,386],additionali:[17,319,387],adenosin:[96,186,273,357],adig:15,advanc:[3,387],advantag:[13,14,387],after:[1,4,7,8,12,13,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,386],aftter:11,again:[3,13],against:[91,179,268,350],aggerg:[60,152,240,324],aggreg:121,agnost:[11,12],algorithm:[5,91,107,147,179,196,268,282,319,350,368],align:[5,7,15,19,42,51,62,64,66,78,91,94,104,105,114,119,135,144,154,156,158,164,165,166,167,179,184,194,195,203,208,225,232,242,244,246,255,268,271,280,281,288,293,302,309,316,326,328,330,337,350,355,365,366,374,379,386],alignemnt:[5,104,105,194,195,281,365,366],alignemtn:[5,105,195,281,366],all:[3,4,5,7,8,10,11,12,13,14,18,19,38,39,42,43,50,51,52,58,60,62,63,64,65,66,67,68,78,79,87,92,94,95,98,104,108,111,113,114,115,116,119,120,121,131,132,135,136,143,144,145,152,154,155,156,157,158,159,167,168,169,170,176,180,184,185,188,194,197,200,202,203,204,205,208,209,221,222,225,226,231,232,233,240,242,243,244,245,246,247,248,255,264,269,271,272,280,283,286,288,289,290,293,294,305,306,309,310,315,316,317,324,326,327,328,329,330,331,337,338,339,340,346,351,355,356,365,369,372,374,375,376,379,380,382,384,386],allel:367,allevi:19,allow:[7,8,10,11,14,16,17,18,384,386,387],aln:19,along:[5,13,30,31,32,33,34,35,36,57,70,71,73,123,124,125,126,127,128,129,150,161,162,163,213,214,215,216,217,218,219,238,250,251,253,296,297,298,299,300,301,303,322,334,335,336,384,385,387],alphanumer:[1,8],alreadi:13,also:[0,1,5,7,8,12,13,17,18,19,384],altern:[39,43,52,63,65,67,79,95,115,120,136,145,155,157,159,168,185,204,209,222,226,233,243,245,247,256,272,289,294,310,317,327,329,331,338,356,367,375,380,387],although:[7,13,18],alu:[5,101,191,277,362],amazon:7,amion:[102,192,278,363],among:15,amount:7,anaconda:[1,6,7,8,14,386],analys:[19,384],analysi:[3,7,383,386],analyz:3,ani:[3,4,5,7,8,10,11,12,13,14,17,18,19,23,50,54,61,70,71,89,107,143,147,161,162,231,250,251,282,315,319,332,334,335,384,385],annot:[5,7,11,13,19,38,39,41,42,43,51,52,62,63,64,65,66,67,68,71,78,79,87,89,94,95,96,108,114,115,119,120,131,132,134,135,136,144,145,154,155,156,157,158,159,162,167,168,176,178,184,185,186,197,203,204,208,209,221,222,224,225,226,232,233,242,243,244,245,246,247,248,251,255,256,264,267,271,272,273,283,288,289,293,294,305,306,308,309,310,316,317,326,327,328,329,330,331,335,337,338,346,349,355,356,357,369,374,375,379,380,382,384],annot_url:13,annotation_proven:12,anntot:[39,63,65,67,79,132,155,157,159,168,222,243,245,247,256,306,327,329,331,338],anoth:[7,10,13,16,18,387],anyon:[3,4,13,19,384],apart:7,apirl:[5,48,229,313],appar:[11,12],append:[5,8,13],applic:[11,12],appri:[38,39,130,131,132,221,222,304,305,306],approach:[15,387],approxim:[5,7,14,16,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,386],ap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,373,374,375,376,377,378,379,380,381,382],combin:[7,12,15,30,33,123,126,147,213,216,296,299,319],come:[11,12,13,18,19,57,150,238,322],comma:15,command:[1,4,5,7,8,9,11,12,13,17,19,384,386],commandarg:384,commands_fil:13,commands_outfil:13,comment:[4,11,12,13],commit:[4,13],common:[3,7,11,13],commonli:[8,14,19],commun:[0,2,3,7,14,18,19,20,386,387],compani:[57,150,238,322],companion:4,compar:[86,175,263,345],compat:[19,386],compil:[7,57,150,238,322],complement:[8,10,36,57,70,71,73,129,150,161,162,163,219,238,250,251,253,303,322,334,335,336],complet:[4,7,8,13,14,15,147,319,386],complex:[4,5,7,19,101,191,277,362,387],complic:13,compliment:[5,30,31,32,33,34,35,36,70,123,124,125,126,127,128,129,161,213,214,215,216,217,218,219,250,296,297,298,299,300,301,303,334],composit:[266,348],comprehens:[13,39,43,52,63,65,67,79,83,95,96,115,120,132,136,145,155,157,159,168,172,185,186,204,209,222,226,233,243,245,247,256,260,272,273,289,294,306,310,317,327,329,331,338,342,356,357,375,380],compris:[12,81,169,170,258,339,340],comprsi:[80,257],conda:[1,3,6,7,8,9,11,12,16,17,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387],conda_build:1,conda_build_config:1,conda_prefix:384,confid:[28,41,134,211,224,308],config:[15,19,384,386],configfil:384,configur:[7,15,19],congenit:[73,163,253,336],connect:6,consensu:[41,134,224,308],conseqeunc:[68,108,197,248,283,369],conserv:[1,59,91,151,179,239,268,323,350],consid:13,consist:[12,13],consortium:[70,161,250,334],constain:[60,152,240,324],constraint:[53,86,93,102,147,175,181,192,234,263,270,278,319,345,352,363],contain:[1,4,5,7,11,12,13,14,15,17,24,44,45,46,47,83,87,88,100,137,138,139,140,172,182,190,227,228,235,241,249,260,264,265,276,311,312,333,342,353,361,382,383,384,387],content:[3,7,8,12,13,14,53,96,147,186,234,273,319,357,386,387],contig:[61,153,241,325],continu:[3,4,6,7,12,13,18,19,104,194,280,365],contribut:[1,6,7,11,12,19],control:[7,13,60,121,152,240,324],conveni:15,convent:[4,13],convert:[1,24,100,190,249,266,276,333,348,361],cookbook:7,coordin:[4,5,7,11,12,13,14,16,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,386],copi:[5,8,19,104,105,194,195,280,281,365,366],core:7,cormier:2,corner:6,correct:[1,7,8,13,17,385,386],correctli:[1,4,5,7,8,11,12,13],correspond:[4,81,170,258,340],could:[1,7,8,10,14,17,19,384,387],count:[88,177,265,347],cover:384,coverag:15,cpg:[5,8,10,11,12,19,53,147,234,319],cpg_island:10,cpu:15,crai:15,cram:15,cran:384,creat:[0,3,5,6,7,8,10,15,19,39,43,49,52,63,65,67,78,79,95,115,120,142,167,168,222,226,230,233,243,245,247,255,256,272,289,294,314,337,338,383,384,385,386,387],creation:[4,14],creator:18,credenti:[4,13],credit:[11,12],crossmap:[50,92,147,151,186,231,269,319,323,357],crucial:7,cse:[1,4,12,16],csi:[53,60,147,152,234,240,319,324],cumbersom:14,curat:[3,5,7,8,11,12,14,18,19,32,35,36,41,70,73,87,88,89,125,128,129,134,161,163,176,177,178,215,218,219,224,250,253,264,265,267,298,301,303,308,334,336,346,347,349],curl:[13,14],current:[1,6,8,9,10,14,16,17,18,19,383,385],current_repodata:1,customari:387,cut:13,cutoff:5,cytogenom:[70,161,250,334],d109:[96,186,273,357],d527f3eb6b664020cf4d882b5820056f:386,dai:14,daniel:[70,161,250,334],danio_rerio:[21,22,23,24,25,26],data:[0,1,2,3,6,8,11,13,14,15,16,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387],data_package_fil:8,data_script:12,databas:[1,4,7,8,11,12,13,14,16,60,71,96,121,152,162,186,240,251,273,324,335,357,382,384],dataset:[7,11,13,39,53,60,80,132,146,147,152,164,165,166,169,182,183,222,234,240,257,306,318,319,324,339,353,354,382],date:[7,8,11,12,13,14,386],date_str:13,datetim:13,dbsnp:[11,12],dbvar:[110,199,285,371],deafult:17,debug:[1,8],dec:[14,59,118,151,239,292,323],decemb:[19,386],decis:[19,386],declar:[11,12],decod:384,decoi:367,decompos:[12,50,68,90,92,108,143,180,197,231,248,269,283,315,351,369],decompress:4,dedic:15,deem:[5,30,31,32,33,34,35,123,124,125,126,127,128,213,214,215,216,217,218,296,297,298,299,300,301],def:13,defaultdict:13,defin:[5,8,13,37,130,220,304],delet:[1,385],delimit:[44,45,46,47,137,138,139,140,227,228,311,312],depend:[4,5,7,8,11,12,13,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,386,387],depth:15,deriv:[86,175,263,345,367],describ:[11,12],descript:[0,8,11,12,13,15,80,169,257,339,384],design:[1,8,10,11,12,16,119,120,209,293,294,380,384],desir:[5,7,8,10,11,12,17,19,382,383,385,386],detail:[5,7,11,12,13,14,383],determin:[8,13,38,39,131,132,147,221,222,305,306,319],dev:[4,12,13,16,384],develop:[3,7,10,18,19],dict:13,dictionari:13,differ:[4,7,8,12,13,14,15,17,18,19,57,91,150,179,238,268,322,350,384,385,386,387],difficulti:19,digit:13,dimension:384,dir:[13,17,384],dir_path:384,directori:[1,4,6,8,9,10,11,12,13,14,15,16,19,383,384],diseas:[5,30,31,32,33,34,35,71,73,123,124,125,126,127,128,162,163,213,214,215,216,217,218,251,253,296,297,298,299,300,301,335,336],displai:[1,5,9,16,383],distinguish:[11,12,13,16],distribut:[18,86,175,263,302,345,367,384],distrubt:90,dna:[5,7,98,99,101,113,188,191,202,274,275,277,360,362,386],dnm1:15,doc:[10,11,13,15,384],docker:[15,384,387],document:[7,12,15,18,386],doe:[1,3,4,5,6,8,11,13,14,16,18,146,182,183,318,353,354],doesn:[8,13],doi:2,doing:[7,13],domain:[5,11,12,19],domin:5,don:[5,14,19,387],done:[1,4,5,7,8,13,14,15,385,386,387],dont_uninstal:1,dosag:[70,161,250,334],download:[1,4,6,7,8,10,11,12,13,14,16,19,38,39,121,131,132,164,165,166,221,222,305,306,382,386],dpsnp:[56,237],driven:[7,19],drug:[50,143,231,315],dsl:15,due:17,dump:13,duplic:[5,8,103,104,105,193,194,195,279,280,281,364,365,366,384],durat:15,dure:[4,7,8,13,15,147,319,383,384,385,387],dynam:[17,384,387],ea_:12,each:[0,5,7,8,10,11,12,14,15,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384],earli:[57,150,238,322],easi:[1,3,6,7,8,10,11,12,13,19,386],easier:[6,7],easili:[10,13],ebi:[15,367],echo:[10,13,15],ecosystem:[5,7],edit:[96,186,273,357],editor:[4,13],edu:[1,4,12,16,24,58,249,333],eiee:[9,10],either:[4,11,12,17,19,383,384],ejhg2008111:[71,162,251,335],element:[5,101,191,277,362],elif:13,elimin:384,els:[11,12,13],emit:15,empow:3,enabl:[15,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382],encephalopathi:[57,150,238,322],encod:13,encourag:[3,18,19,384,386],end:[4,8,11,12,19,164,165,166,383,386],endswith:[13,15],enforc:16,enough:[11,12,13],ensebml:[306,327,329,331,338],ensembl2ucsc:[213,214,215,216,217,218,219,221,223,225,231,232,234,238,240,242,244,246,248,250,251,253,255,263,269,270,271,283,284,286,287,288,293,296,297,298,299,300,301,303,305,306,309,310,315,316,317,319,322,326,327,328,329,330,331,334,335,336,337,338,345,351,352,355,356,369,372,373,374,375,379,380],ensembl:[7,10,11,12,19,30,31,32,33,34,35,36,37,39,41,44,45,46,54,55,57,59,61,70,71,73,80,81,85,87,88,89,91,96,100,101,103,104,105,107,118,123,124,125,126,127,128,129,130,132,134,136,137,138,139,145,148,149,150,151,153,155,157,159,161,162,163,168,169,170,174,175,176,177,178,179,181,183,185,186,190,191,193,194,195,196,204,207,209,213,214,215,216,217,218,219,222,226,227,233,234,238,240,243,245,247,250,251,253,256,263,270,272,287,289,294,296,297,298,299,300,301,303,306,310,311,317,319,322,324,327,329,331,334,335,336,338,345,352,354,356,373,375,380,386],ensembl_v1_dir:7,ensembl_v1_fil:7,ensur:[1,7,8,12,13,385],enter:[1,8,13,385],entrez:13,entri:[14,23,332],enumer:13,env:[0,1,7,8,9,10,14,16,18,19,385,386],env_var:13,env_var_fil:13,environ:[0,1,7,8,9,11,12,13,15,16,18,383,384,385,386,387],environment:15,environmnet:386,epilepsi:[57,150,238,322],epilept:[57,150,238,322],equal:[38,39,131,132,221,222,305,306],error:13,esearch:13,esp6500si:[10,12,58],esp:[10,12],essenti:[13,384],etc:[10,11,12,13,19,42,51,62,64,66,78,88,94,114,119,135,144,154,156,158,167,177,184,203,208,225,232,242,244,246,255,265,271,288,293,309,316,326,328,330,337,347,355,374,379],etyp:13,euo:15,eutil:13,evalu:15,even:19,everi:[13,14,19],everyon:[3,386],everyth:[11,12,13,15],evolutionari:[59,151,239,323],evs:[12,58],evs_bulk_data:12,exact:[5,17],exactli:13,exampl:[0,3,15,18,19,164,165,166,386],except:[5,13,14,104,105,194,195,280,281,365,366],exclud:[7,13,98,188,386],exclus:[11,12,37,130,220,304],execut:[1,7,8,14,385,386],executor:15,exist:[7,8,11,13,14,15,382,384,386],exit:[1,5,8,9,10,11,12,13,15,16,17,383,385],exmapl:387,exom:58,exon:[38,39,63,64,65,81,88,94,95,131,132,155,156,157,170,177,184,185,221,222,243,244,245,258,265,271,272,305,306,327,328,329,340,347,355,356],expand:384,expect:[4,13,86,175,263,345,384],experi:[14,19,384],explain:[11,12],expr:384,express:[3,11,14,382,383,384],expression_analysi:384,extens:[4,5,12,32,35,125,128,215,218,298,301],extent:387,extra:[4,11,13],extract:[3,4,7,8,11,12,13,14,36,71,129,162,219,251,303,335,384,386],extref:[36,73,129,163,219,253,303,336],f15e697a24cd2fa0ce42d4a7682ae2:8,facilit:2,fai:[5,7,10,15,29,74,76,77,84,98,99,113,116,117,122,173,187,188,189,202,205,206,212,261,274,275,290,291,295,343,358,359,360,376,377,386],fail:[1,13,39,43,52,63,65,67,79,95,115,120,222,226,233,243,245,247,256,272,289,294,386],fall:1,fals:[15,21,22,23,24,25,26,27,28,56,58,69,72,90,97,106,121,160,210,211,237,249,252,266,302,332,333,348,367,381,384],fam83d:15,faq:[24,249,333],faqformat:[24,249,333],far:13,fast:7,fasta:[5,7,10,11,12,15,19,21,22,25,26,29,84,97,98,99,106,113,116,117,122,173,187,188,189,202,205,206,212,261,274,275,290,291,295,343,358,359,360,367,376,377,381,386],fastq:[74,76,77],fatal:[57,150,238,322],fcgi:13,featur:[18,30,31,32,33,34,35,36,51,52,57,70,71,73,80,123,124,125,126,127,128,129,144,145,150,161,162,163,169,175,181,182,213,214,215,216,217,218,219,232,233,238,250,251,253,257,296,297,298,299,300,301,303,316,317,322,334,335,336,339,345,352,353],feb:[1,5,14,91,96,177,186,268,273,347,357,381],fetch:7,few:[3,15,18,57,150,238,322,384],field:[3,13],fifth:7,fil:210,file:[0,1,4,5,7,9,11,12,13,14,16,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387],file_1:8,file_2:8,filenam:384,fill:[4,7,13,19,386],filter:[10,38,39,130,131,132,221,222,304,305,306],fin:15,final_command:13,find:[0,3,7,15,19,383,384,385,386],finder:[5,107,196,275,282,360,368],fine:17,finish:[1,4,8],first:[4,7,11,12,13,18,57,150,238,322],five:[119,120,208,209,293,294,379,380],five_prime_utr:[119,120,131,184,208,209,293,294,305,355,379,380],fix:[1,8,13,14],flag:[1,7,9,11,12,16,17,21,22,23,24,25,26,27,28,38,39,56,58,69,72,90,97,106,113,121,131,132,160,202,210,211,221,222,237,249,252,266,302,305,306,332,333,348,367,381,382,385],flexibl:7,focus:[19,386],follow:[1,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,30,31,32,33,34,35,123,124,125,126,127,128,213,214,215,216,217,218,296,297,298,299,300,301,383,385,386],forc:13,forg:[11,12,19,386],fork:[3,6],form:[4,7,13,19,146,182,183,318,353,354,386],format3:[24,249,333],format:[4,5,7,8,11,12,13,15,16,24,28,42,51,54,59,60,62,64,66,78,89,90,94,100,101,103,109,114,119,135,144,148,151,152,154,156,158,167,178,184,190,191,19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199,204,207,209,213,214,215,216,217,218,219,221,223,225,231,232,234,238,240,242,244,246,248,249,250,251,253,254,255,263,269,270,271,276,283,284,286,287,288,293,296,297,298,299,300,301,303,305,306,309,310,315,316,317,318,319,322,326,327,328,329,330,331,333,334,335,336,337,338,345,351,352,354,355,356,361,367,369,372,374,375,379,380,382],ncreat:13,necessari:[3,4,7,10],necessarili:7,need:[1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,384,385,386],neither:[17,175,181,345,352],netxflow:387,neural:14,neuro:[60,121,152,240,324],never:17,new_summari:13,newli:1,next:4,nextflow:7,nextflowvers:15,nhlbi:58,nih:[5,11,13,14,30,31,32,33,34,35,70,123,124,125,126,127,128,161,213,214,215,216,217,218,250,296,297,298,299,300,301,334,382],nist:[75,254],nlm:[5,11,13,14,30,31,32,33,34,35,70,123,124,125,126,127,128,161,213,214,215,216,217,218,250,296,297,298,299,300,301,334,382],nnat:15,nnn:13,noarch:[1,7,8,11,12,386],noe:5,nomeclatur:[36,129,219,303],non:[5,8,14,17,18,24,51,52,60,70,71,80,83,84,87,88,94,95,100,103,121,144,145,152,161,162,169,172,173,176,177,184,185,190,193,232,233,240,249,250,251,257,260,261,264,265,266,271,272,275,276,279,316,317,324,333,334,335,339,342,343,346,347,348,355,356,360,361,364],noncod:[83,84,172,173,260,261,342,343],none:[11,12,13,15],normal:[7,8,12,13,14,18,50,68,90,92,108,143,180,197,231,248,269,283,315,351,369,384],notch:384,note:[1,4,5,6,7,8,14,16,17,18,20,147,319,384,386],notic:[8,14],notif:8,nounset:[1,16],nov:[5,15,85,262],novo:18,now:[1,4,6,10,12,13,15,18,19],npars:13,nrc1299:[36,129,219,303],nrc:[36,129,219,303],nsampl:384,nucleotid:[5,7,84,99,116,117,173,187,189,205,206,261,274,290,291,343,358,359,376,377],nucletodi:[5,85,174,262,344],number:[5,7,8,12,13,14,15,384],numer:384,numpi:[1,147,319],observ:[86,175,263,345],obtain:[11,12,19,39,43,52,63,65,67,79,95,115,120,222,226,233,243,245,247,256,272,289,294,384],occur:[57,150,238,322],occurr:[7,13],oct:[41,103,130,134,169,178,193,207,224,279,304,308,339,349,364,378],octob:[5,44,45,46,47,49,227,228,230],off:384,offer:19,offici:3,often:5,omim:[5,30,31,32,33,34,35,71,123,124,125,126,127,128,162,213,214,215,216,217,218,251,296,297,298,299,300,301,335],omit:[18,384],omnibu:[3,11,14,382,384],onc:[1,3,4,5,6,7,8,11,12,13,18,19,21,22,23,24,25,26,27,28,56,58,69,72,90,97,106,121,160,210,211,237,249,252,266,302,332,333,348,367,381,382],one:[4,6,7,8,10,12,13,14,15,16,17,18,19,57,150,238,322,384,386,387],onli:[1,4,5,7,8,9,11,12,13,14,16,17,19,60,78,121,152,167,240,255,324,337,384,385,386],onto:[19,386],open:[4,13,19],openssl:121,option:[1,5,8,9,10,11,12,15,16,17,383,384,385],order:[1,4,5,6,7,8,10,11,12,13,14,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385],org:[1,2,38,39,50,68,92,96,108,111,121,131,132,143,180,186,197,200,221,222,231,248,269,273,283,286,305,306,315,351,357,369,372,384],organ:13,origin:[3,6,11,12,16,36,39,70,73,129,161,163,219,222,250,253,303,334,336],ostrand:[9,10],other:[3,4,7,8,10,11,12,13,14,16,19,21,22,23,24,25,26,27,28,42,43,51,52,56,58,66,67,69,72,78,79,90,97,106,114,115,119,120,121,135,136,144,145,158,159,160,167,168,203,204,208,209,210,211,225,226,232,233,237,246,247,249,252,255,256,266,288,289,293,294,302,309,310,316,317,330,331,332,333,337,338,348,367,374,375,379,380,381,384,386],otherwis:[13,17,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,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,360,376,377,381],sanit:12,sann:384,sat:1,save:[4,13],scaffold:[5,7,39,43,44,45,46,47,52,54,61,63,65,67,70,71,79,87,88,89,95,99,101,107,115,120,136,137,138,139,140,145,148,153,155,157,159,161,162,168,178,185,187,189,204,209,222,226,227,228,233,235,241,243,245,247,250,251,256,264,265,272,274,277,282,289,294,306,310,311,312,317,327,329,331,334,335,338,356,358,359,375,380],scafold:46,scale:384,scholarli:3,scientif:[3,7,18],scientist:[3,7,19],score:[1,5,91,104,105,179,194,195,268,280,281,350,365,366],scratch:[1,15],script1:11,script2:11,script3:11,script:[0,1,3,7,10,11,12,14,15,18,383,384,386,387],script_path:13,scripts_path:13,scroll:5,search:[0,3,7,8,10,14,15,17,18,71,162,251,335,385,386],search_term:5,second:[7,13],secondari:[59,151,239,323],section:5,sed:13,see:[0,1,3,4,5,6,7,8,9,10,11,12,13,14,15,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386],seen:[18,19],seg:[103,193,279,364],segdup:[103,193,279,364],select:[6,20,53,130,147,234,304,319],selenocystein:[39,63,64,65,94,95,132,155,156,157,184,185,222,243,244,245,271,272,306,327,328,329,355,356],self:[5,13,14],sensit:[1,8,70,161,250,334],sep:384,separ:[5,8,13,14,15],seper:11,sept:[70,161,250,334],seq:[42,51,62,64,66,78,94,114,119,135,144,154,156,158,167,184,203,208,225,232,242,244,246,255,271,288,293,309,316,326,328,330,337,355,374,379],seqcov:15,seqcover_background:15,seqcover_report:15,seqeunc:[5,41,87,98,113,134,176,188,202,224,264,266,275,308,346,348,360,386],sequenc:[5,7,15,24,41,58,74,76,77,90,91,98,99,100,101,103,113,134,164,165,166,179,187,188,189,190,191,193,202,224,249,268,274,276,277,279,308,333,350,358,359,361,362,364,386],seri:[11,13,14,382,384],servic:18,set:[1,3,5,7,8,9,10,11,12,13,15,16,19,21,22,23,24,25,26,27,28,30,33,36,38,39,42,43,51,52,56,57,58,62,63,64,65,66,67,69,70,71,72,73,78,79,90,94,95,97,106,114,115,119,120,121,123,126,129,131,132,135,136,144,145,150,154,155,156,157,158,159,160,161,162,163,167,168,184,185,203,204,208,209,210,211,213,216,219,221,222,225,226,232,233,237,238,242,243,244,245,246,247,249,250,251,252,253,255,256,266,271,272,288,289,293,294,296,299,302,303,305,306,309,310,316,317,322,326,327,328,329,330,331,332,333,334,335,336,337,338,348,355,356,367,374,375,379,380,381,384],sever:[57,150,238,322],sgk2:15,share:[1,7,8,10,14,16,17,18,386],shell:[15,384],should:[1,3,4,8,11,12,13,17,18,147,319,384],show:[0,1,5,7,8,9,10,11,12,14,15,16,17,18,19,384,385,386,387],show_recip:16,shown:[5,275,360],side:[13,14],sign:6,silent:[13,14],similar:[3,5,8,9,11,14,147,319,385],simpl:[7,13,15,101,191,277,362,384,387],simpli:[7,8,10,11,13,382],simplifi:[7,386],simrep:[5,107,196,282,368],sine:[5,101,191,277,362],singl:[0,5,8,10,11,13,14,19],singular:[15,384,387],site:[7,13,14,90,96,112,186,201,210,211,237,252,273,287,357,373,386],situat:7,sixth:7,size:[4,5,7,14,16,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261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show-env","Snakemake Workflow with GGD","ggd uninstall","Using GGD","Using GGD in Workflows"],titleterms:{"1000g":[27,28,90,97,106,210,211,302,367],"138":[56,237],"case":386,"final":18,"new":[4,13],Use:[10,386],Using:[1,5,8,9,10,11,12,16,17,19,383,385,386,387],access:[7,14,18,382],acid:[29,102,122,192,212,278,295,363],activ:[21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382],add:18,addit:[1,5,8,9,10,11,12,16,17,19,383,385],all:[9,187,358],altern:384,amino:[29,102,122,192,212,278,295,363],annot:[83,146,172,182,183,260,318,342,353,354],approach:384,argument:[1,5,8,9,10,11,12,16,17,383,385],associ:[50,92,143,180,231,269,315,351],autosom:[30,31,32,33,34,35,123,124,125,126,127,128,213,214,215,216,217,218,296,297,298,299,300,301],avail:[7,20],base:5,bash:[4,13],bedp:[109,198,284,370],berg:[30,31,33,34,123,124,126,127,213,214,216,217,296,297,299,300],blekhman:[30,32,33,35,123,125,126,128,213,215,216,218,296,298,299,301],broad:[27,28,56,72,210,211,237,252],build:[4,5],bwa:302,cancer:[36,129,219,303],canon:[37,38,39,130,131,132,220,221,222,304,305,306],capabl:7,caveat:14,ccd:[41,134,224,308],ccdg:[40,109,133,198,223,284,307,370],cds:[42,43,135,136,225,226,309,310],chain:[82,104,105,171,194,195,259,280,281,341,365,366],chang:[102,192,278,363],channel:386,check:[1,4,13,18],chr22:[74,76,77,164,165,166],chr:[29,83,84,116,117,122,146,172,173,182,183,205,206,212,260,261,290,291,295,318,342,343,353,354,376,377],chrom:[44,45,46,47,137,138,139,140,227,228,311,312],chromsiz:[17,48,49,141,142,229,230,313,314],cite:2,cli:[4,13],clingen:[70,161,250,334],clinic:[50,143,231,315],code:[51,52,53,94,95,117,144,145,147,184,185,206,232,233,234,271,272,291,316,317,319,355,356,377],combin:5,command:[0,10,14,18],complex:12,conda:[10,14,386],configur:386,consensu:[146,318],consist:7,constrain:[53,147,234,319],contribut:[3,4,386],cpg:[54,148,235,320],creat:[1,4,11,12,13,14,18],creation:7,curat:13,cytoband:[55,149,236,321],dang:[71,162,251,335],danrer10:[23,24,25],danrer11:26,data:[4,5,7,9,10,12,17,18,19,20],databas:[110,199,285,371],dbsnp:[56,237],differ:[5,9,10,16],directori:17,domain:[89,178,267,349],domin:[30,31,32,123,124,125,213,214,215,296,297,298],dup:[103,193,279,364],eiee:[57,150,238,322],ensembl2refseq:[44,137],ensembl2ucsc:[227,311],ensembl:[21,22,23,38,42,50,51,62,64,66,68,69,78,82,92,94,98,108,111,113,114,119,131,135,143,144,154,156,158,160,167,171,180,184,188,197,200,202,203,208,221,225,231,232,242,244,246,248,255,269,271,283,286,288,293,305,309,315,316,326,328,330,332,337,351,355,369,372,374,379],env:383,environ:[10,14,17,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,34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56,157,167,168,244,245,255,256,328,329,337,338],island:[54,148,235,320],isoform:[37,130,220,304],known:[80,169,257,339],knowngen:[81,170,258,340],lab:[53,96,147,186,234,273,319,357],liftov:[82,171,259,341],list:[9,16,19],lncrna:[83,84,172,173,260,261,342,343],local:[4,13],main:13,make:[1,11,12],manag:7,map:[44,45,46,47,137,138,139,140,227,228,311,312],meta:[7,8,11,13,14,17,382],microsatellit:[85,174,262,344],missens:[86,175,263,345],mm10:381,more:12,multipl:8,name:10,ncbi:[44,45,46,47,49,87,88,137,138,139,140,142,176,177,201,227,228,230,264,265,266,311,312,314,346,347,348,373],nextflow:[15,387],omni:[27,210],omnibu:13,one:5,onli:[10,42,43,66,67,114,115,119,120,135,136,158,159,203,204,208,209,225,226,246,247,288,289,293,294,309,310,330,331,374,375,379,380],origin:[4,13],ostrand:[57,150,238,322],output:[10,384],packag:[5,7,8,9,10,19,20],path:17,pattern:9,pfam:[89,178,267,349],phase1:[28,211],phase3:90,phastcon:[91,179,268,350],phenotyp:[92,180,269,351],pkg:16,pli:[93,181,270,352],polya:[182,353],predict:[17,183,354],prefix:[8,9,10,14,16,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382],previous:18,privat:18,protein:[94,95,117,184,185,206,271,272,291,355,356,377],pseudogen:[146,318],python:13,quick:19,quinlan:[53,147,234,319],radar:[96,186,273,357],recess:[33,34,35,126,127,128,216,217,218,299,300,301],recip:[1,4,7,8,11,12,13,14,16,17,18,382],refer:[21,22,25,26,97,98,99,113,187,188,189,202,274,275,358,359,360,381],refin:5,refseq2ensembl:[45,138],refseq2ucsc:[228,312],refseq:[24,87,88,100,176,177,190,249,264,265,266,276,333,346,347,348,361],region:[29,53,83,84,116,117,122,146,147,172,173,182,183,205,206,212,234,260,261,290,291,295,318,319,342,343,353,354,376,377],repeat:[107,196,282,368],repeatmask:[101,191,277,362],repo:[4,13],repositori:18,result:[5,15],run:[1,15],same:5,score:[86,93,102,175,181,192,263,270,278,345,352,363],script:[4,13],search:[5,19],segment:[103,193,279,364],self:[104,105,194,195,280,281,365,366],sequenc:[29,84,106,116,117,122,173,205,206,212,261,290,291,295,343,367,376,377],set:6,shell:10,show:383,sifrim:[73,163,253,336],simpl:[5,10,11,12,107,196,282,368],snakemak:[384,387],snp:[27,28,210,211],somat:[108,197,283,369],specif:[5,9,14],standard:12,stanford:[96,186,273,357],start:19,step:15,store:18,structur:[109,110,111,112,198,199,200,201,284,285,286,287,370,371,372,373],submit:[4,13],success:[8,385],support:13,svs:[75,254],term:5,test:[13,14],time:[5,14],tool:386,toplevel:[113,202],transcript:[38,39,114,115,116,117,131,132,203,204,205,206,221,222,288,289,290,291,305,306,374,375,376,377],trna:[118,183,207,292,354,378],two:5,ucsc2ensembl:[46,139],ucsc2refseq:[47,140],ucsc:[24,25,26,37,41,54,55,59,61,80,81,85,87,88,89,91,100,101,103,104,105,107,110,118,130,134,148,149,151,153,169,170,174,176,177,178,179,190,191,193,194,195,196,199,207,220,224,235,236,239,241,249,257,258,259,262,264,265,266,267,268,275,276,277,279,280,281,282,285,292,304,308,320,321,323,325,333,339,340,341,344,346,347,348,349,350,360,361,362,364,365,366,368,371,378,381],uninstal:[18,385],updat:[4,13],used:1,using:[1,4,5,8,9,10,13],utr:[119,120,208,209,293,294,379,380],valid:1,variabl:[19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,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