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.
SNP calling from RNAseq data
Do I need to do Indel Realignment and Base Recalibration while calling SNP from RNAseq data?
If yes, then please share the command line.
What are the parameter that should be used for raw VCF filtering?
Please also share any documents/text related to SNP calling from RNAseq as well as DNAseq with command lines.