Generate contact maps #215
Description
Description of feature
Some use cases for read-mapping are:
- studying read coverage
- variant calling
- getting a contact map
Variant-calling is too complex to be done via in a read-mapping pipeline and has been offloaded to sanger-tol/variantcalling, nf-core/sarek, and sanger-tol/variantcomposition.
Read coverage has been implemented - #171
Contact maps could be implemented by taking sub-workflows from the other sanger-tol pipelines via our modules repository.
We'd want to support both Cooler and Pretext outputs.
To support generating combined maps (maps of all haplotypes together), we will need an option to control the inclusion or not of multi-mapped reads. Unless we it's ok to display multi-mapped reads even when there is a single haplotype ?