If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
MuTect2 tumor only mode: empty VCFs
I am trying to run Mutect2 in tumor only mode without a matching normal. However, when I did this, MuTect2 produced output VCFs that had a full header, but had no variant calls.
Here is a sample command that I ran to produce variant calls for chromosome 1:
module load gatk/3.5.0; java -Xmx10g -Djava.io.tmpdir=$TMP -jar GenomeAnalysisTK.jar -T MuTect2 -R $REFERENCE_GENOME_FA --dbsnp $DBSNP_VCF --cosmic $COSMIC_VCF -dt NONE --input_file:tumor $TUMOR_BAM --intervals chr1:1-249250621 -o $OUTPUT_VCF
Note: I ran a similar command to this (same input files, etc.) using MuTect v1.1.4 and it produced a complete VCF.
Can you please explain if there is anything I need to change?