We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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?