This discussion will focus on commands/tools we can use to check and validate our output files at each step in a sequence processing pipeline and make sure they don’t have any obvious problems. Given how broad in scope this topic is, we will use the Morrell lab’s sequence_handling pipeline to guide the discussion. This pipeline is intended to process sequence data from raw FASTQ files all the way up through GATK’s SNP calling best practices workflow and returns a VCF file ready for downstream analysis.

Please read the following prior to the discussion:

• If you are not familiar with our pipeline, please skim through the main README page: sequence_handling.

Slides from this discussion are available on the DoesNaughtCompute Github page here.