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.
HaplotypeCaller missing a clear variant
I am comparing two callers and found some cases in which HC behaves strangely.
Let's look into one of the cases. There's a site in which there are 15 bases overlapping. Of these, 6 are like the reference (C) and 9 are variants (T). Please, look at the attached IGV's snapshot. The reads are of good quality; same for the bases. And there are no indels nor mismatches around. How is it possible that HC genotypes this site as 0/0?
20 60216651 . C . . . AN=2;DP=14 GT:AD:DP:RGQ 0/0:6:14:0
These are the running parameters:
-T HaplotypeCaller --genotyping_mode DISCOVERY -ERC BP_RESOLUTION -R human.fasta --dbsnp dbsnp_138.vcf.gz --ploidy 2 -o output.gvcf.gz -I input.bam
-T GenotypeGVCFs -R human.fasta --includeNonVariantSites --dbsnp dbsnp_138.vcf.gz --variant output.gvcf.gz -o output.genotypes.gvcf.gz
I am using GATK version v3.4-0-g7e26428