I would be grateful for your advice on bcftools calling issue I am having. I have 3 bam files and following changes I see in the genome browser at a particular location.
- REF -> ALT
- G -> GT (in first two bams)
- G -> GA (in third bam)
Visually they look clean and no issues. When I call individually all changes are detected properly. But when calling jointly by
bcftools mpileup the
G->GT is detected but
G->GA is not and more disturbingly the genotype for the 3rd bam is marked as
0/0 . There seem to be no heterozygous sites here.
bcftools norm with reference did not fix it.
The commands used are
bcftools mpileup -a AD -f ref.fa -P Illumina bam1.bam bam2.bam bam3.bam| bcftools call --ploidy-file Ploidy.txt --multiallelic-caller --variants-only
Thanks so much!