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.
BwaAndMarkDuplicatesPipelineSpark Input Format
Hi, looking forward to GATK_4 release, so I have started investigating 4 beta1. I like the tools that are available, calling method and Spark! I had therefore set up a Spark pipe of BwaAndMarkDuplicatesPipelineSpark and BQSRPipelineSpark: very handy, would be cool if there was a pipeline for BWA + MD + BQSR. My issue is with BwaAndMarkDuplicatesPipelineSpark which specifies input as BAM/SAM/CRAM, this seems odd. Is fastq not an option? I ran with 2 fastq (R1, R2) as input and got the error:
Sorry, we only support a single reads input for spark tools for now
I know this is a beta, but can someone explain why input to alignment is in aligned format? I tried merging PE reads into a single fastq, and using just R1.fastq.
Appreciate any input on this,