Description of feature
When browsing the multi-genome CRAM file, it may be useful to have some genomic context. But gene annotaiton files may not be available. At least, the pipeline could run tantan or windowmasker, and produce some BED files that can be loaded in the IGV. In addition, it could also run the self-alignment of the target to itself, and produce a coverage plot, that would allow to see the shadow of repeats and duplications.
Description of feature
When browsing the multi-genome CRAM file, it may be useful to have some genomic context. But gene annotaiton files may not be available. At least, the pipeline could run tantan or windowmasker, and produce some BED files that can be loaded in the IGV. In addition, it could also run the self-alignment of the target to itself, and produce a coverage plot, that would allow to see the shadow of repeats and duplications.