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Question of single calling and total calling
Lyc
CHNMember ✭
Hello:
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.
Lyc
Best Answer
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Geraldine_VdAuwera
Cambridge, MA admin
In the first case, Sample A had some very small evidence for a second alternate allele, C. But G/C is very unlikely to be the true genotype according to the allele depth and the PL and GQ values.
When you do joint calling on them (second case), the genotypes are evaluated over the population (of only 2 samples, but they are treated like a population). Now that we know that the G allele is also present in Sample B, we estimate that it is much more likely that Sample B is just homozygous for G and that the C allele we observed was just an artifact.
Ideally you want to have more samples in your population so that if there really is a C that is a minority allele, you would see it in another sample and still be able to call it; and if it's not real, you would be more confident about calling your samples homozygous for G. As it stands now you have a confident (PASS) variant call because it's clear there is some variation at this site, but the genotype calls themselves are low-confidence, probably due to low depth and low quality of the sequence data at this site.
Answers
In the first case, Sample A had some very small evidence for a second alternate allele, C. But G/C is very unlikely to be the true genotype according to the allele depth and the PL and GQ values.
When you do joint calling on them (second case), the genotypes are evaluated over the population (of only 2 samples, but they are treated like a population). Now that we know that the G allele is also present in Sample B, we estimate that it is much more likely that Sample B is just homozygous for G and that the C allele we observed was just an artifact.
Ideally you want to have more samples in your population so that if there really is a C that is a minority allele, you would see it in another sample and still be able to call it; and if it's not real, you would be more confident about calling your samples homozygous for G. As it stands now you have a confident (PASS) variant call because it's clear there is some variation at this site, but the genotype calls themselves are low-confidence, probably due to low depth and low quality of the sequence data at this site.