Mutect2: mitochondria mode weird

Follow

Roberto Sirica

• June 03, 2020 14:46

Hello all, I'm trying to call variants for mitochondrial samples using gatk v.4.1.2.0 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

0

• 

  David Benjamin

  • June 09, 2020 03:01

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

  0

  Comment actions Permalink
• 

  Roberto Sirica

  • June 09, 2020 07:50

  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 

  0

  Comment actions Permalink

Please sign in to leave a comment.