Mutect2 failing to produce F1R2.tar.gz and stat files on TCGA bams (tumor-normal pairs)
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3 months ago
tb_2020 • 0

I am using GATK version 4.1.9.0 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.

next-gen mutect2 • 177 views
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