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!
Where to download BAM files required for PON in Mutect2 worksheets given for Workshop 1803
I am beginner and have just started using GATK. I was following the worksheets for Workshop 1803, specifically the worksheet on Mutect2 basics. There is an exercise on PONs, and it requires HG00190.bam, NA19771.bam and HG02759.bam. These are not provided with the Gatk Bundle of the workshop. When i rand the commands, I got the error "unable to read non-existent file." I read in the worksheet that these are retrieved from 1000 genomes and I was able to track down the locations of files corresponding to them, but they are all CRAM files. All of them have sizes around 3 GB, whereas the normal and tumor bam files (provided in the bundle) are only of around 250 MB size. I have the following queries -
1. Is there any link to download the BAM files directly ?
2. Should I download the CRAM files and convert them to BAM ?
The links that I have found for these are the following -
HG00190 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/FIN/HG00190/exome_alignment/
NA19771 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/MXL/NA19771/
HG02759 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/GWD/HG02759/