I'm using gkno's 'fastq-vcf' pipeline as a way to run a serial of steps for variant calling. gkno allows the use of bash streams to pipe data between tools without ever writing to disk.
I was wondering if there is away to keep the BAM alignment coming out of "left-align-indels" step in this pipeline. I can see these three steps are writing to the stream: "filter-bam", "realign-gaps", "left-align-indels"
And "variant-call"(freebayes) is the receptor of the final stream. I would like to instead save the intermediary BAM file for further visualization and analysis. If this is possible, do you think this change would cause a big performance hit?
I did look at bamleftalign's(tool used for "left-align-indels" step), it seems like the only option is to write to the stream. Is that right?
That's a good suggestion. I might have to integrate 'tee' as a tool in gkno. If I do, that could meant I can easily grab the stream coming out of tools which currently only write to the stream.
Thanks, I will explore this option.