a) GATK version used : gatk-220.127.116.11
b) Exact GATK commands used :
gatk Mutect2 -R ref.fa -L chrM --mitochondria-mode -I input.bam -O output.vcf
gatk FilterMutectCalls -R ref.fa -autosomal-coverage 10 --mitochondria-mode -V output.vcf -O output_filtered.vcf
Hi GATK team,
I am using Mutect2 on rat mitochondrial DNA samples and I need to compute the genotype dosage information of the called variants for further analysis with Plink2.
In the output vcf file, I don't see any field that would allow me to do so.
The annotations I have are :
INFO : CONTQ=93;DP=207;ECNT=1;MBQ=20,20;MFRL=84,87;MMQ=60,60;MPOS=11;OCM=0;POPAF=2.40;SEQQ=1;STRANDQ=3;TLOD=0.923
FORMAT : GT:AD:AF:DP:F1R2:F2R1:SB
The only likelihood information I see is the TLOD but from my understanding it is not enough to get the dosage.
Is there a way to get the GP or DS information with mutect2, which are the fields compatible for Plink2 to import dosages ? Or more generally is there anyway to get dosage information from the output of Mutect2
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