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.
UnifiedGenotyper Genotype Calling Oddity
I encountered a strange issue with GATK calling. For instance, a mutation below has VAF of ~49%, but somehow was called by GATK as HOM.
This happens quite a few times where a 45% mutation is sometimes is called as WildType etc. I understand that GATK chooses the genotype that has the highest probability likelihood, so a 50% VAF wildtype is in theory possible, but I don’t see how that can happen so often.Have you experienced this type of problem before? Below is the cmd line I used. Any suggestions of what may have happened? Thanks much in advance.
java -Djava.io.tmpdir=MK1029_PN011_20140314/Temp/ -Xmx20g -jar GenomeAnalysisTK-2014.3-17-g0583018/GenomeAnalysisTK.jar -nt 5 --allSitePLs -L MK1029rs48snp.bed -glm SNP -R unmasked_hg19.fasta -T UnifiedGenotyper --output_mode EMIT_ALL_SITES -D dbSNP137.hg19.vcf -stand_call_conf 0.0 -rf MappingQuality -mmq 20 -stand_emit_conf 0.0 -dcov 100000 -o all.vcf -I bamfile1 –I bamfile2 –bamfile3 etc.