Samtools : what is threshold for the mapping quality?

Question

[Govardhan Anande]

Hie friends,

I am new to samtools, however I used samtools for calling variants for study and I found out that I am getting reference allele depth for alternate allele but that respective alternate allele is not reported in alt allele column. For more details, I visualize that sample in samtools tview, over there I am getting blue dot instead of alt allele but in read depth am gettion alt allele.

Then I degraded the mapping quality by giving -q 0 -Q 0 (i.e. samtools mpileup -D -B -u -C 0 -q 0 -Q 0 -f Ref | bcftools view -gc - > vcf), still am not getting that alt allele.

Please suggest/comment regarding this issue, also let me know if am not clear about the problem.

Thanks in advance