Mercurial > repos > ulfschaefer > phe_samtools_mpileup

annotate phe_samtools_mpileup.sh @ 10:f78ed0f61f52 draft

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author ulfschaefer
date Mon, 21 Dec 2015 10:17:45 -0500
parents 65b5406977c9
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/bin/bash
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2
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3 echo $@
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4
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5 BAM=$1
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6 shift
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7 REF=$1
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8 shift
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9 OUTVCF=$1
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10
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11 CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF"
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12
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13 echo "CMD: "$CMD
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14 eval $CMD