Hi everyone! I'm carrying out variant calling using
bcftools. First, I created .mpileup file using
bcftools mpileup, then run
bcftools calls for variant calling. In some positions .mpileup file contains information about both alleles of diploid heterozygous (e.g. A,T while reference only T), but when I run
bcftools calls this information erased and only one allele remained.
Also, I used IGV-browser, it showed that it is heterozygous, but final .vcf file does not contain both alleles, only one of them. See the attachments. Who knows why it is happening, I tried to use most arguments of bcftools call, but the result is the same. By the way, it only happened in a bunch of positions, most positions worked fine as expected.
Interested position circled in blue
dac.calls.vcf contains only G, but must contain both A and G