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.
1000genomes exomes and VQSR
I've processed an Illumina exome with BWA, and I've made SNP and indel calls with HaplotypeCaller. In the VCF there are lots of variations (100k more or less) but I suppose it can be filtered out with VQSR.
My question is: where could I download the bam exomes from 1000Genomes in order to process them with my exome data another time with HaplotypeCaller and be able to filter variations with VQSR. I'm new and I don't know what bams should I use from 1000Genomes.
The reference sequence is hg19, downloaded from the GATK bundle.
Thank you very much,