Question of single calling and total calling
I met a question when I used the GATK pipeline.
When I perform single calling for my Sample A & B, I get the results like:
Sample A Chr01 2245 . A C,G 171.31 PASS ... GT:AD:DP:GQ:PL 1/2:0,1,6:7:1:221,202,199,19,0,1
Sample B Chr01 2245 . A G 192.84 PASS ... GT:AD:DP:GQ:PL 1/1:0,8:8:18:221,18,0
These results are different.
However, when I perform total calling for these two samples simultaneously, at that chromosone-position, I get this result:
Chr01 2245 . A G 387.43 . .... GT:AD:DP:GQ:PL 1/1:0,6:7:18:220,18,0(A) 1/1:0,8:8:18:221,18,0(B)
So that the SNP of Sample A is no longer C/G but just a G.
I don't clearly know how it works out.
Thanks for any help from your team.