Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Mutect2: mitochondria mode weird



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    David Benjamin

    aa_change is not a Mutect2 annotation.  What is the output of Mutect2 at this site?

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    Roberto Sirica

    I annotated the vcf with VEP, aa_change is a field from vep annotation, I paste the line from the original Mutect file :

    chrM 3461 . G A DP=91;ECNT=6;MBQ=37,37;MFRL=171,209;MMQ=60,60;MPOS=36;OCM=0;POPAF=2.40;TLOD=346.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1

    my concern is that I know by other molecular tecniques that there is a variant in chrM 3460 that is pathogenic. This variant  seems like is "1-based" with respect to the pathogenic variant, because the aa change moved to "0-based" is right while it is not correct with this annotation.

    I apologize if I'm not so clear. Thanks for your support 

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