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annotate scripts/createBamFromResults.sh @ 0:1955f03f092e

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author biomonika <biomonika@psu.edu>
date Tue, 02 Sep 2014 14:16:04 -0400
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biomonika <biomonika@psu.edu>
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1 #!/bin/bash
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biomonika <biomonika@psu.edu>
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2 set -e;
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biomonika <biomonika@psu.edu>
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3 #example usage: ./createBamFromResults list_of_sequences bam_file outfile reference
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biomonika <biomonika@psu.edu>
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4 #creates small bam files containg only sex-linked genes and their corresponding reads
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biomonika <biomonika@psu.edu>
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5
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biomonika <biomonika@psu.edu>
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6 list_of_sequences=$1;
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biomonika <biomonika@psu.edu>
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7 bam_file=$2;
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biomonika <biomonika@psu.edu>
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8 outfile=$3;
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biomonika <biomonika@psu.edu>
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9 reference=$4
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biomonika <biomonika@psu.edu>
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10
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biomonika <biomonika@psu.edu>
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11 samtools view -h -o out.sam $bam_file;
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biomonika <biomonika@psu.edu>
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12 grep -f $list_of_sequences out.sam >igv;
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biomonika <biomonika@psu.edu>
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13 cat igv | sort -r >$outfile;
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biomonika <biomonika@psu.edu>
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14 samtools view -bS $outfile | samtools sort - ${outfile%????};
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biomonika <biomonika@psu.edu>
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15
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biomonika <biomonika@psu.edu>
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16 rm -f igv out.sam;