Mutect2: mitochondria mode weird
Hello all, I'm trying to call variants for mitochondrial samples using gatk v.18.104.22.168 with Mutect2 mitochondria mode, with the command line below:
java -jar gatk Mutect2 -R genome.fa --mitochondria-mode -I mybam.bam -O myoutvcf.vcf
I observed a strange behaviour, the resulting variants seems to be shifted of one base, I try to explain:
chrM 3461 aa_change=A52D
this variant annotated shows this aminoacidic change, but if I visualize it in IGV and look at the reference sequence it seems that the correct base is the next one on forward direction because only with the ocmbination of nucleotides of the following base we can obtain tath type of genetic variation. How is it possible?
Thank you in advance
aa_change is not a Mutect2 annotation. What is the output of Mutect2 at this site?
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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