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.
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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.
I have a question how to create Panel of Normals (PON) using Mutect2: do we still need to add the dbSNP and Cosmic parameters when running the following command for each normal BAM in artifact_detection_mode? Will command lines with/without dbSNP and cosmic affect the PON VCF calling?
"java -jar GenomeAnalysisTK.jar \
-T MuTect2 \
-R reference.fasta \
-I:tumor normal1.bam \
[--dbsnp dbSNP.vcf] \
[--cosmic COSMIC.vcf] \
[-L targets.interval_list] \