The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.