Hi, I use gatk188.8.131.52 and find a strange alignment in mutect2 outout bam, I think the red T on the right of indel seems to should be aligned to the left T in the indel.
I am not sure what you mean. Can you post the original BAM file screenshot and the VCF records for the two variants?
there is only one records this variant
original bam screenshot from markduped bam
I see. So, you are saying the tool is not calling the T as a variant, but you think it should? Can you check the base qualities at the site for the T? Can you also color the reads by sample and post an IGV screenshot?
Hi, MuTect2 called this T as a variant
the called variant is "7 55242469 . TTAAGAGAAGCAACATCTC T", by this called variant, the ALT T should be aligned to the first T of the REF,
but, from the first screenshot, which is from MutTect2 output bam, the ALT T is aligned to the last C of the REF
Oh, I think I see what you are asking. The variant is a deletion. Deletions are represented in the VCF by the position before the start of the deleted sites. In this case, the alt T is the T at the beginning of TTAAGAGAAGCAACATCTC. I hope this answers your question. Sorry if I am misunderstanding.
so， why in the first screenshot, the red T did not align to the first T of TTAAGAGAAGCAACATCTC
Why do you think the red T shoul align to the first T in the indel? It is nowhere near the beginning of the indel. Perhaps the HaplotypeCaller and Indel Realignment slide decks may help. They are in the presentations section.