[Samtools-help] samtools confused genotype

[郑竹清 <zz...@12...>]

Hi all,

I found the genotype is also available for the sites which without any reads passed my quality filter criterion. for example, the genotype is 1/1 but without any reads 1/1:0,0,0:0:0:0:0,0,0,0:0,0. So why does samtools report results like that, whether these sites should be marked as ./. .

My command is as follow (version 1.31)
samtools mpileup -q 20 -t DP,DPR,DV,DP4,INFO/DPR,SP -g -f ref.fa -b bam.list | bcftools call -V indels -v -c -O z -o raw.vcf.gz

Can you give me some suggestions on how to deal with these sites?

best


Zheng zhuqing