Mercurial > repos > biomonika > linkyx

annotate LINKYX_mpileup_wrapper.sh @ 25:ffe50d004cb4

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samtools sort, echo path
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 22:01:22 -0400
parents 7997c93ee479
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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22
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
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1 #!/bin/bash
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
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2 results=$1;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
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3 bam_file=$2;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
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4 reference=$3;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
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5
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
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6 sorted_bam=${bam_file}_sorted
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
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7
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
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8 samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results