Mercurial > repos > biomonika > linkyx

annotate LINKYX_mpileup_wrapper.sh @ 4:0979980b5bdc

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edited README file
author biomonika <biomonika@psu.edu>
date Fri, 20 Feb 2015 14:50:31 -0500
parents 0d8315be76b7
children
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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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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 samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results