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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,