GitHub - alexpenson/scripts

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Name		Name	Last commit message	Last commit date
Latest commit History 64 Commits
#summary.r#		#summary.r#
.gitignore		.gitignore
1p_combine.pl		1p_combine.pl
1p_combine.sh		1p_combine.sh
AnnotCosmic.sh		AnnotCosmic.sh
CalculateHsMetrics.sh		CalculateHsMetrics.sh
GGP-Tumor-Normal-TView.sh		GGP-Tumor-Normal-TView.sh
GGP-Tumor-Normal-TView.sh~		GGP-Tumor-Normal-TView.sh~
Open3.pl		Open3.pl
Open3_test.pl		Open3_test.pl
README		README
ReduceReads.qsub		ReduceReads.qsub
SAVI.fmt		SAVI.fmt
SAVI2bed.awk		SAVI2bed.awk
SAVI_sequential.sh		SAVI_sequential.sh
SAVI_sequential.sh~		SAVI_sequential.sh~
SAVI_to_CRAVAT.pl		SAVI_to_CRAVAT.pl
SAVI_to_CRAVAT.sh		SAVI_to_CRAVAT.sh
SAVI_to_vcf.pl		SAVI_to_vcf.pl
SamToFastq		SamToFastq
SnpEff_to_MutSig.R		SnpEff_to_MutSig.R
VarScan_1p.sh		VarScan_1p.sh
VarScan_copynumber_MDS.sh		VarScan_copynumber_MDS.sh
VarScan_position.sh		VarScan_position.sh
add_filename_column		add_filename_column
add_flag_to_id		add_flag_to_id
allele_freq_strelka_snpEff.pl		allele_freq_strelka_snpEff.pl
ann_bed.R		ann_bed.R
ann_bed.R~		ann_bed.R~
annotate.sh		annotate.sh
bam_add_eof.py		bam_add_eof.py
bam_add_eof.py~		bam_add_eof.py~
bam_flag.pl		bam_flag.pl
bam_flag.pl~		bam_flag.pl~
bashrc		bashrc
bed2segs		bed2segs
blasr.sh		blasr.sh
blast_to_fasta		blast_to_fasta
blastn.sh		blastn.sh
bowtie-paired-genome-transcriptome,sh		bowtie-paired-genome-transcriptome,sh
bowtie-paired-genome-transcriptome.sh		bowtie-paired-genome-transcriptome.sh
bowtie-paired-mapped-sam.sh		bowtie-paired-mapped-sam.sh
bowtie-paired-single-virus-pipes-par.sh		bowtie-paired-single-virus-pipes-par.sh
bowtie-paired-single-virus-pipes.sh		bowtie-paired-single-virus-pipes.sh
bowtie-paired-single-virus.sh		bowtie-paired-single-virus.sh
bowtie-paired-unmapped.sh		bowtie-paired-unmapped.sh
bowtie-single-virus-pipe.sh		bowtie-single-virus-pipe.sh
bowtie-single-virus-pipes.sh		bowtie-single-virus-pipes.sh
bowtie-unmapped-plus-bam.sh		bowtie-unmapped-plus-bam.sh
bowtie-unmapped.sh		bowtie-unmapped.sh
bowtie2.qsub		bowtie2.qsub
build_prior.sh		build_prior.sh
bwa.sh		bwa.sh
chr		chr
chr_ncbi_to_ucsc.sed		chr_ncbi_to_ucsc.sed
coverageBed.sh		coverageBed.sh
createDB_gffutils.py		createDB_gffutils.py
curl10		curl10
cut_in_half.sh		cut_in_half.sh
deltat		deltat
expand_annovar_exons.awk		expand_annovar_exons.awk
ext.sh		ext.sh
fasta_qual_to_fasta.pl		fasta_qual_to_fasta.pl
fastq2id		fastq2id
fastq_to_fasta		fastq_to_fasta
fastq_to_fasta_qual.pl		fastq_to_fasta_qual.pl
fastqqual		fastqqual
fastqseq		fastqseq
fill.pl		fill.pl
fill.pl~		fill.pl~
format_del.pl		format_del.pl
format_del.sh		format_del.sh
fpfilter.pl		fpfilter.pl
gene_subset.sh		gene_subset.sh
grepf.awk		grepf.awk
hist.r		hist.r
history.py		history.py
make_picard_region_file.sh		make_picard_region_file.sh
mart_range.R		mart_range.R
meganormal_to_vcf.pl		meganormal_to_vcf.pl
mutate.awk		mutate.awk
neither_mapped		neither_mapped
normal.r		normal.r
normal.sh		normal.sh
normal2.r		normal2.r
patients.R		patients.R
plot.r		plot.r
plot2.r		plot2.r
pos2segs		pos2segs
progress.sh		progress.sh
qualrange		qualrange
rand.r		rand.r
random_fasta.r		random_fasta.r
random_string.sh		random_string.sh
range.R		range.R
rows-to-columns.awk		rows-to-columns.awk
sam2fasta		sam2fasta
sam2fastq		sam2fastq
sam2pos		sam2pos
sam_header_size		sam_header_size

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Scripts for manipulating alignment files, tables etc.
Written in shell, R, python...

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