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.
GenotypeGVCFs liftOver problem?
I am trying to run GenotypeGVCFs on my combined gvcf file 'cohort.g.vcf' and i am getting the following error:
A USER ERROR has occurred: Given reference file does not have data at the requested contig(ChroChromosome01)!
I don't understand why this is happening as i used the same reference genome for all previous steps (such as variant calling,CombineGVCFs). Do i need to liftOver genomic coordinates on the VCF file based on the reference genome? I am trying to use flo to get the chain file for my reference genome and then use that chain file as input to picard tool liftOverVCF or liftOvervariants?. I'm just not sure why i have to do this as the vcf should match the reference genome coordinates as i am using the same reference throughout. Please help