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.
Genotyping for dbSNPS
In a project I need see the allelic frequency for dbSNPs in the RNAseq data of a single cell. To be precise, given the dbsnp I need 0/0s as well if there is required coverage of reads. SNV calling pipeline normally does not report if it is 0/0. I have come all the way to recalibrated BAM following the RNAseq SNV calling best practice as suggested in GATK site. Help with the command would be highly appreciated.