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
There is not a way to incorporate a "no call" in a VCF that I am aware of, and this is not something you usually see outside of genotypes from microarray experiments. The reason you don't see a "0/0" call is probably because you have only one sample in your VCF file. If you have two samples in your file, and at a particular site sample1 is heterozygous variant and sample2 is not, then you would have sample1 = 0/1 and sample2 = 0/0. If you were to include non-variant sites in your VCF, then you would be reporting the entire reference genome, plus your variant sites. This is not what VCF is for.