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