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…m.nih.gov/pmc/articles/PMC8190613/ and add as filtering option in region_filter.py to partially address COMBAT-TBgh-2
…r masking variants
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@biominer I'm finally getting around to reviewing this PR. The Modlin et al paper links to a CSV file on Zenodo but the regions seem to differ from the BED file that you provided. Here is the start of the BED file I computed from the Zenodo CSV: (note that this is BED, so coordinates are zero-based, half-open) |
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Added the bed file and edited region_filter.py and the README.md accordingly to add and document the option for masking variants in the regions of systematic low coverage/poor mappability reported by Modlin et al. In response to #2 .