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Mutect2 vcf FORMAT field
I’m trying to use Mutect2 (GATK version 3.7) for somatic mutation calling.
I noticed that if I use it with the default parameters in the FORMAT field I have the following informations:
If I add the annotation modules, for example -A FisherStrand and -A StrandOddsRatio, the FORMAT field contain only GT:AD:AF.
This is my command line:
java -jar GenomeAnalysisTK.jar -T MuTect2 \
-R reference.fasta \
-I:tumor tumor.bam \
-I:normal normal.bam \
--dbsnp dbsnp_138.hg19.vcf \
--cosmic hg19_cosmic_v54_120711.vcf \
-o output.vcf \
-L targets.interval_list \
-A FisherStrand \
-A StrandOddsRatio \
Thank you very much!