Setting up automated processing of fastq files from WES
I will continue to add to this to require only a single input. This input will be a list of file names and paths to fastqs.
I also plan to have options for filtering methods, ie. pedigree input file and filtering strategy. Currently it can be used to filter each sample against all others in a joint genotyped vcf or lone genotyping and produces output for:
- functional variants (dominant diseases).
- Bialleic variants.
- Homozygous varaints.
A batch process will also be added to simplify grouping.