A Snakemake powered pipeline developed to perform variant-effect-prediction and frequency analysis given multiple Variant Call Format datasets. This has been developed in partial fulfilment of a MSc in Bioinformatics at the University of Pretoria by Graeme Ford.
Remove unnecessary variant renaming step. Variant renaming is now done during the LIFTOVER rule of the Vcf-Validation sub-pipeline only.
Changes to FILTER rule:
Change filter stringency for samples and variants.
Allow autosomal chromosomes only.
Remove steps to filter out variants where the reference allele in the .vcf file does not match that of the reference genome. This step was unnecessary since variant reference alleles are altered to match that of the reference genome during the LIFTOVER rule of the Vcf-Validation sub-pipeline.
Change variant nomenclature specifications for linkage-disequilibrium pruning step.
Ensure that chromosome output is kept consistent by adding the --output-chr chr26 flag to all plink commands.
Changes to
ALL_COLLATErule:LIFTOVERrule of theVcf-Validationsub-pipeline only.Changes to
FILTERrule:Change filter stringency for samples and variants.
Allow autosomal chromosomes only.
Remove steps to filter out variants where the reference allele in the
.vcffile does not match that of the reference genome. This step was unnecessary since variant reference alleles are altered to match that of the reference genome during theLIFTOVERrule of theVcf-Validationsub-pipeline.Change variant nomenclature specifications for linkage-disequilibrium pruning step.
Ensure that chromosome output is kept consistent by adding the
--output-chr chr26flag to all plink commands.