I am using GATK version 22.214.171.124 to do somatic variant calling on TCGA BAMs.
Mutect2 does not produce any f1r2.tar.gz or stat files (--f1r2-tar-gz argument is included as below) when I ran the following command on TCGA BAMs.
gatk --java-options "-Xmx6G" Mutect2 -R file.fasta \ -I NORMAL_DNA.bam \ -I TUMOR_DNA.bam \ -normal NORMAL \ --germline-resource $RESOURCE \ --f1r2-tar-gz file.tar.gz \ -O file.vcf.gz
I see no error messages.
How can I resolve this issue? When I ran the same script on a non-TCGA BAMs, it worked just fine. Is this a TCGA specific issue? I would appreciate any inputs/suggestions. Thank you.