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 on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
getPileupSummaries input for hg38
Hi- I would like to run
getPileupSummaries on bam files aligned against hg38. Do you have any recommendation about what vcf input to use for hg38?
The docs relative to getPileupSummaries suggest using gnomAD which is based on hg19. Would you suggest using that after lifting them over to hg38?
Alternatively, one could use dbSNP common but dbSNP vcf don't have the
AF field. They do have a
CAF field which seems promising after some parsing, here's the description
An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter
Either way, there seem to be no off-the-shelf input for hg38. Any thought much appreciated!