| Previous changeset 9:17996fd454c6 (2015-12-21) Next changeset 11:714a4c13d64c (2015-12-21) |
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Commit message:
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modified:
phe_samtools_mpileup.sh |
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| diff -r 17996fd454c6 -r f78ed0f61f52 phe_samtools_mpileup.sh --- a/phe_samtools_mpileup.sh Mon Dec 21 09:00:43 2015 -0500 +++ b/phe_samtools_mpileup.sh Mon Dec 21 10:17:45 2015 -0500 |
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| @@ -8,14 +8,7 @@ shift OUTVCF=$1 -# TMPBAM=$$.tmpbam -# TMPBAM2=$$.tmpbam2 -# samtools view -bS $SAM > $TMPBAM -# samtools sort $TMPBAM $TMPBAM2 - CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF" echo "CMD: "$CMD eval $CMD -# rm $TMPBAM -# rm $TMPBAM2.bam |