Different panels detect the same site, there are two different annotations, somatic and germline
I used mutect2 to detect mutations, and used FilterMutectCalls to detect mutations. The first time I used a panel to detect mutations, the site was somatic mutation (PASS), but the second time I used another new panel to detect the same site change. Become a germline, how could this be? The difference between the results of vcf is only in the GERMQ score. How is this score calculated?I use a single tumor sample。
chr1 26773390 . G A . germline AS_FilterStatus=SITE;AS_SB_TABLE=390,344|442,383;DP=1602;ECNT=1;GERMQ=1;MBQ=20,20;MFRL=173,176;MMQ=60,60;MPOS=36;POPAF=3.61;ROQ=93;TLOD=2017.98 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:734,825:0.536:1559:207,266:229,242:461,533:390,344,442,383
chr1 26773390 . G A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=390,344|442,383;DP=1602;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=173,176;MMQ=60,60;MPOS=36;POPAF=3.61;ROQ=93;TLOD=2017.98 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:734,825:0.536:1559:207,266:229,242:461,533:390,344,442,383
It is expected that you might get slightly different results when using a different panel of normals because different PONs may contain different variants. The GERMQ score is the quality score for a variant existing in the germline, based on the panel of normals. The different GERMQ scores are likely coming from a variant being present in one of your panels but not the other. Does this help explain your results?
I use the same pon, but the bed file for mutect2 to detect mutations is different. Does this have an impact?
Okay, thank you for clarifying. Yes, using any difference in input files is expected to impact how Mutect2 works and may result in differences in mutations that are detected. I am not sure what bed files you are using or what is different between them, but it is expected to get different results if you use different files. You can read more about the algorithms for Mutect2 here as well as this FAQ about how Mutect2 detects mutations.
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