I have called the mutation in Human NGS data follow the samtools/bcftools mpileup call, and got the VCF files. Due to the false positive, I need to go further filter, just like filter the position with more than 20 reads support, Or the remove the variants frequency less than threshold value, (eg: AF < 4% ).
The VCF file from bcftools call do not contain the INFO/AF tags, so I add it with below command:
bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t AF
But after AF added, I only got two kinds of AF values for my variants records, both AF =1 for GT 1/1, and AF=0.5 for GT 0/1.
It seems AF in samtools in not the same concept in GATK tools? with GATK I can get the AF for the site = alt reads / reads depth, and in samtools, I only got the AF value = AC/AN, here AC is always reported as 1 and AN is 1 or 2 in my samples.
May be some mistakes need to be pointed out?