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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
HaplotypeCaller on all dbSNP positions
I'm running HaplotypeCaller on whole-genome data. I'm interested in only several thousand specific positions across the genome, all of which are in dbSNP. Some of these are indels, which makes me more inclined to use HaplotypeCaller. However, I want to know the quality/likelihood of the bases called at each position in downstream analysis. So, my goal is to obtain a VCF file containing a call at every dbSNP position, whether or not it's variant with respect to the reference. I need each associated with a likelihood from VQSR, with VQSLOD having the same meaning whether or not the site is variant.
It seems that I could do this with UnifiedGenotyper --output_mode EMIT_ALL_CONFIDENT_SITES. How can I replicate this with HaplotypeCaller? Second, is there a better way to achieve this? Should I not be using HaplotypeCaller at all?
So far, I ran HaplotypeCaller with --emitRefConfidence BP_RESOLUTION --dbsnp dbsnp.vcf, followed by GenotypeGVCFs --includeNonVariantSites --dbsnp dbsnp.vcf. However, the rsIDs aren't used to populate the ID column in the resulting VCF (is this a bug?), so I can't then remove non-dbSNP positions. Secondly, annotations aren't added to positions matching the reference.
Thanks in advance.