Explore discarding positions based on sequencing depth #410
Description
Mutations are currently being discarded at a given position due to low depth, but the depth values at those positions are still included in downstream depth-based calculations.
The parameter mutation_depth_threshold is applied at mutation level but does not modify the depth data. The idea is that if a mutation is discarded due to the depth threshold, then the depth should be set to 0 for that mutation in that sample.
The mutation_depth_threshold is being used in the SUBSETMAF module. All variants with depth <= the determined threshold are discarded but no file with the discarded mutations is generated.
To do
- Save discarded mutations due to low depth into a file.
- Add those positions to the bed file with flagged variants to be removed from the depth files from the sample in which the specific mutation was removed.