Coverage can be very variable across certain genomes due to collapsed repeats, and variability in the sequencing. Rather than skipping regions when the coverage is too high, Platypus should automatically down-sample coverage per-sample, to a sensible level.
This is already implemented for the alternative haplotype selection model, so it should be straightforward to implement this.
Coverage can be very variable across certain genomes due to collapsed repeats, and variability in the sequencing. Rather than skipping regions when the coverage is too high, Platypus should automatically down-sample coverage per-sample, to a sensible level.
This is already implemented for the alternative haplotype selection model, so it should be straightforward to implement this.