Mercurial > repos > biomonika > linkyx
diff scripts/createBamFromResults.sh @ 9:695d28139f3e
toolshed8
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Tue, 09 Sep 2014 14:31:02 -0400 |
| parents | 1955f03f092e |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/createBamFromResults.sh Tue Sep 09 14:31:02 2014 -0400 @@ -0,0 +1,16 @@ +#!/bin/bash +set -e; +#example usage: ./createBamFromResults list_of_sequences bam_file outfile reference +#creates small bam files containg only sex-linked genes and their corresponding reads + +list_of_sequences=$1; +bam_file=$2; +outfile=$3; +reference=$4 + +samtools view -h -o out.sam $bam_file; +grep -f $list_of_sequences out.sam >igv; +cat igv | sort -r >$outfile; +samtools view -bS $outfile | samtools sort - ${outfile%????}; + +rm -f igv out.sam; \ No newline at end of file