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nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
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Re-add ROI support for WES #75

Closed nvnieuwk closed 1 year ago

nvnieuwk commented 1 year ago

Description of feature

ROI support has for now been disabled due to the addition of goleft_indexsplit. This should be solved in a new creative way

nvnieuwk commented 1 year ago

https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html Compute coverage per region with the -d flag. Write a script that divides the BED into multiple other BED files of even coverage

matthdsm commented 1 year ago

bedtools coverage == mosdepth but much slower

nvnieuwk commented 1 year ago

That's what I thought too, but mosdepth doesn't retain the original regions of the ROI file which was a big nope for me

nvnieuwk commented 1 year ago

Added in #92