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#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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