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!
BQSR non overlapping contigs error
I am trying to run BQSR and I'm getting the non overlapping contigs error that seems to come from mismatched reference and known sites vcf files. My code is below. What I'm trying to figure out is how I can tell which files are matched. I tried the gnomAD exome vcf, which to my understanding is hg19, but apparently not the same format. My reference genome is from UCSC. I have downloaded dbSNP 151 but I expect that will be NCBI format so I'm not sure that will help. Can you offer some guidance on which files match and how to tell?
Also, in terms of documentation, it would be helpful if the tool doc mentioned that the .vcf needs to be indexed.
gatk BaseRecalibrator \
-I $SCRATCH/active/memtest2/SRR112728.marked_duplicates.sorted.bam \
-R $WORK/hg19.fa \
--known-sites $WORK/gnomad.exomes.r2.1.1.sites.vcf.bgz \
Thanks very much,