Homozygous Ref calls and no calls

[ashkot]

Hi all, I was wondering if someone could help.

I am generating a vcf file based on the following command chain.

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

What is being observed is that the VCF file only contains "1/1" or "0/1" or "1/0" calls. I don't see a single "0/0" call.

In bcftools i have tried to eliminate a the "v" parameter but then i dont get any genotype calls.

What I am really after is: is there a way that i can generate another VCF file (or include in the same file) that also has "0/0" genotypes. Also, is is possible to include no call, i.e. a way to indicate if a site was not sequenced at all?

Thanks in advance. A

[etorstenson]

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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