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Old 08-09-2012, 11:01 AM   #2
etorstenson
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Location: Tennessee

Join Date: Jun 2012
Posts: 10
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You definitely don't want -v in your bcftools view call, it hides those invariant sites.

samtools mpileup -uf referencegenomefile eg2.sorted.bam | bcftools view -cg - | perl /usr/share/samtools/vcfutils.pl varFilter -D100 > results.vcf

When you do this, though, they homozygous ref aren't written as 0/0, they appear as follows:
21 9411856 . G . 60 . DP=61;VDB=0.0124;AF1=0;AC1=0;DP4=19,30,0,12;MQ=39;FQ=-57;PV4=0.012,0.041,2.2e-06,1 PL 0
21 9411868 . C . 71 . DP=65;VDB=0.0124;AF1=0;AC1=0;DP4=23,30,0,12;MQ=39;FQ=-68;PV4=0.0053,1.6e-18,1.2e-06,1 PL 0
21 9411871 . G . 65 . DP=62;VDB=0.0124;AF1=0;AC1=0;DP4=22,28,0,12;MQ=39;FQ=-62;PV4=0.0051,5.2e-26,1.1e-06,1 PL 0
21 9411931 . G . 79 . DP=42;VDB=0.0003;AF1=0;AC1=0;DP4=18,20,0,4;MQ=48;FQ=-76;PV4=0.12,1,0.00024,0.24 PL 0
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