It would be great to have a single machine script showing how to go from FASTQ to VCF. I've done something similar for rnaseq pipelines at treehouse so that partners can get started very easily:
I'd be happy to test/iterate/develop a similar Makefile if you kick start by dumping a history of command line histories plus link to a publicly available FASTQ sample. Ideally this same sample would have been run through some other pipelines for comparison as well.
It would be great to have a single machine script showing how to go from FASTQ to VCF. I've done something similar for rnaseq pipelines at treehouse so that partners can get started very easily:
https://github.com/UCSC-Treehouse/pipelines/blob/master/Makefile
I'd be happy to test/iterate/develop a similar Makefile if you kick start by dumping a history of command line histories plus link to a publicly available FASTQ sample. Ideally this same sample would have been run through some other pipelines for comparison as well.