This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Mutect2 output not match to real situation
I used Mutect2 to call variants on a pair of tumor and normal samples. One variant "PASS" the filter is shown below:
4 6956086 . C CTTTCTTGCT . PASS ECNT=1;HCNT=34;MAX_ED=.;MIN_ED=.;NLOD=54.49;RPA=1,2;RU=TTTCTTGCT;STR;TLOD=17.08 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:543,19:4.673e-03:0:0:.:9520,0:163:122
To my limited understanding of Mutect2 output, I think passing the filter means that "CTTTCTTGCT" is in tumor, not normal. I am trying to locate this small insertion event, and I attached an screenshot of the BQSR bam file, with the variant in the middle of the sequence. Here is one read I got from the tumor sample's sam file. Overall, there is a C to T mutation, which also occurs in the normal sample (not shown), but I do not see this insertion when comparing to the reference
ST-E00545:65:HJLYWALXX:7:1221:18061:39844 83 4 6956047 60 150M = 6955995 -202 CGCTCCTGTTCATGGACAGGTTTGTGGCTGCTTTCTTGCTTTTCTTGCTGTTGGAACTGGAGACTTAACTGGAAGCAGAGTCTTTCCTGCGTGTAGCTTTGACAGCATGTGACCGTCGGCCTTGGTTGGGCTGAGGTGTTTCTGTGGGTC JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA NM:i:1 MD:Z:39C110 AS:i:145 XS:i:22 RG:Z:032017
The reference around chr4 6956096 is "CTTTCTTGCCTTTCTTGCT".
I am new to Mutect2 so I want to confirm with you experts about this. I understand that MuTect2 is still in beta testing stage, but I would really appreciate your advice. Thanks a lot!