Mercurial > repos > biomonika > linkyx

annotate LINKYX_mpileup_wrapper.sh @ 22:7997c93ee479

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last attempt to install perl as part of linkyx
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 19:40:01 -0400
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22
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
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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>
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3 bam_file=$2;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
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4 reference=$3;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
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5
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
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6 sorted_bam=${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