Mercurial > repos > biomonika > linkyx

annotate LINKYX_mpileup_wrapper.sh @ 0:1955f03f092e

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initial commit
author biomonika <biomonika@psu.edu>
date Tue, 02 Sep 2014 14:16:04 -0400
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children ea52ef8d7f3a
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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 results=$1;
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biomonika <biomonika@psu.edu>
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3 bam_file=$2;
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biomonika <biomonika@psu.edu>
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4 reference=$3;
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biomonika <biomonika@psu.edu>
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5
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biomonika <biomonika@psu.edu>
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6 sorted_bam=${bam_file}_sorted
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biomonika <biomonika@psu.edu>
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7
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biomonika <biomonika@psu.edu>
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8 #LINKYX_PATH set during toolshed installation
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biomonika <biomonika@psu.edu>
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9
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biomonika <biomonika@psu.edu>
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10 samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results
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biomonika <biomonika@psu.edu>
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11
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biomonika <biomonika@psu.edu>
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12 #samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt