Entering edit mode
9.0 years ago
897598644
▴
100
Excuse me:
After calling variants with GATK, the result showed 0/1. But when I confirmed the variants using bam files with samtools, it showed . or , with high depth (more than 100). Is that normal?
Best!
Dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand. Any mismatches will be represented by "ATCG" and "atcg" on forward and reverse strand respectively. Look at the AD tag in the VCF file. It should give you counts for reads supporting the reference allele and the alternate alleles. If you have decent read counts for both the alleles, than 0/1 is normal.
The AD tag is 121,84. But the position in the bam files were all dot or comma. Did not they contradict?
This is clearly a heterozygous mutation based on the AD tag. I am not sure why you aren't seeing the mismatch or the SNP. What kind of variant is it? SNP or indel ? What are you using pileup or tview?
It is SNP, i used the command like:samtools mpileup -q0 -Q0 -AB -f.
Use samtools tview.
The results of samtools tview matched that of samtools mpileup