If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
dbSNP VCF for BQSR
We are planing to work on GRCh38, and BQSR requires dbSNP VCF as input.
The latest one is v146 in GRCh38 here
There are two files in dbSNP, one is ALL_20151104.vcf (3.2G) and another is common_all_20151104.vcf (0.9G). Which one should we use? Should we just take the file as is, or do we need some filtering (say MAF, multiallielic SNP, etc)