Why Does Mpileup Skip some variants ?
when I make variant call with bcftools mpileup and call , i can't get some variants,especially those have the same number of Ref and Mutant reads!!!
My command is :
bcftools mpileup -Ou -f ref my.sorted.bam | bcftools call --ploidy 1 -mv -Ov -o my.vcf
I can't find this variant in my vcf :
T (Ref: with depth=94) ---> C (Variant: with depth=94)
This variant exist in IGV but i can't find it in my vcf.