SNPfiltR {SNPfiltR}

SNPfiltR: A package for interactively visualizing and filtering SNP datasets

Description

The SNPfiltR package allows users to interactively visualize the effects of relevant filters on their datasets in order to optimize filtering parameters rather than simply following historical precedent. Each function takes a variant call format (vcf) file, stored in local memory as a vcfR object, as input. Most functions can be run without specified cutoffs, in order to visualize the distribution of the parameter of interest in your given dataset. Then the same function can be run with a specified cutoff, and a filtered vcfR object will be returned. For detailed documentation and vignettes showing fully implemented SNP filtering pipelines, please go to: devonderaad.github.io/SNPfiltR