Variants of Interest

Output Directory: results/variantsOfInterest/

Rules

• VariantsOfInterest.smk

  • mpileupVariantsOfInterest

  • AlleleBalanceVariantsOfInterest

Introduction

In some biological systems, it may be useful to perform surveillance on mutations which we are interested in. For example, this could be to detect drug-resistance markers in Plasmodium parasites, or insecticide-resistance mutations in the malaria mosquito.

If provided with a table of user-defined variants of interest, RNA-Seq-Pop can calculate allele frequencies at these sites from the aligned read data, and plot the results.

Results