Hello all, I'm trying to call variants for mitochondrial samples using gatk v.220.127.116.11 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
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