Updated README.md

README.md

@@ -10,7 +10,7 @@ This repository provides support for SVision downstream CSV filter and analysis.
 
 Please install pandas, numpy and [intervaltree](https://pypi.org/project/intervaltree/). 
 
-The call set for the paper is under ./supports.
+The call set for the paper is ./supports/HG00733.svision.s5.graph.vcf.
 
 #### Prepare config file
 
@@ -30,7 +30,7 @@ The config file requires:
 
 
 ```
-python FilterMain.py -v svision.vcf -g graph_exact_match.txt -w ./workdir -i 0,3
+python FilterMain.py supports/HG00733.svision.s5.graph.vcf -g ./supports/HG00733.graph_exactly_match.txt -w ./output_dir -i 0,3
 ```
 
 This will generate three files:
@@ -39,5 +39,5 @@ This will generate three files:
 
 *prefix*.Raw-CSVs.tsv: SVision CSVs filtered by graph structures.
 
-*prefix*.HQ-CSVs.tsv: CSVs additionally filtered by simple repeats.
+*prefix*.HQ-CSVs.tsv: CSVs additionally filtered by tandem repeats.
 

supports/HG00733.HQ-CSVs.tsv

@@ -0,0 +1,80 @@
+chr1	43593624	43594257	522	10	48.03	SINE
+chr1	70446312	70446751	676_1	4	66.29	SINE
+chr1	81194666	81195870	748	12	57.14	LINE
+chr1	175231433	175232798	1167	12	33.19	LTR
+chr1	187495696	187497594	1219	15	21.6	LTR
+chr1	205209504	205209664	1311	18	0.0	None
+chr1	246817940	246819350	1677	20	21.56	SINE
+chr2	16225124	16225236	2006	22	0.0	None
+chr2	45061833	45079498	2140	23	21.25	LINE
+chr2	61473618	61476320	2214	12	11.36	SINE
+chr2	65600546	65601136	2242	6	100.0	Retroposon
+chr2	116216766	116224724	2555	14	33.02	LINE
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+chr5	155906888	155907080	7472	47	100.0	DNA
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+chr11	126632640	126632771	14670	29	0.0	None
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+chr12	25106528	25107673	15025	47	20.26	DNA
+chr12	39466255	39466532	15134	15	46.21	DNA
+chr12	65424994	65425174	15289	29	100.0	LINE
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+chr14	65375820	65376415	17087	15	50.42	SINE
+chr14	65791559	65791687	17091	5	0.0	None
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+chr17	34854678	34855853	19449	12	9.28	DNA
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+chr20	61329281	61329476	22123	2	0.0	None
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+chr22	18136755	18146780	22983	28	8.71	LTR
+chr22	20075212	20075748	23001	6	50.93	SINE

supports/HG00733.svision.s5.graph.Raw-CSVs.tsv

@@ -0,0 +1,262 @@
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