diff --git a/README.md b/README.md index 3c9943a..a8d70bd 100644 --- a/README.md +++ b/README.md @@ -7,11 +7,12 @@ This tool offers multiple options for filtering variants (in VCF files, relative It currently has 5 main modes: 1. Filter by region. Mask out variants in certain regions. Region lists available as: - 1. `farhat_rlc` and `farhat_rlc_lowmap`: Refined Low Confidence (RLC) and RLC plus low mappability regions from [Marin et al](https://doi.org/10.1093/bioinformatics/btac023) - 1. `pe_ppe`: PE/PPE genes from [Fishbein et al 2015](https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981) - 2. `tbprofiler`: [TBProfiler](http://tbdr.lshtm.ac.uk/) list of antibiotic resistant genes - 3. `mtbseq`: [MTBseq](https://github.com/ngs-fzb/MTBseq_source) list of antibiotic resistant genes - 4. `uvp`: [UVP](https://github.com/CPTR-ReSeqTB/UVP) list of repetitive loci in M. tuberculosis genome + 1. `modlin_ibs` : Illumina Blind Spots (IBS) from [Modlin et al 2021](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000465) + 2. `farhat_rlc` and `farhat_rlc_lowmap`: Refined Low Confidence (RLC) and RLC plus low mappability regions from [Marin et al](https://doi.org/10.1093/bioinformatics/btac023) + 3. `pe_ppe`: PE/PPE genes from [Fishbein et al 2015](https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981) + 4. `tbprofiler`: [TBProfiler](http://tbdr.lshtm.ac.uk/) list of antibiotic resistant genes + 5. `mtbseq`: [MTBseq](https://github.com/ngs-fzb/MTBseq_source) list of antibiotic resistant genes + 6. `uvp`: [UVP](https://github.com/CPTR-ReSeqTB/UVP) list of repetitive loci in M. tuberculosis genome 2. Filter by proximity to indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site. 3. Filter by percentage of alternate allele bases. 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FarhatLab_RLC_Regions, FarhatLab_RLC_LowMap_Regions, MTBseqRegions, @@ -31,6 +32,7 @@ from . import Filter REGIONS = { + "modlin_ibs": Modlin_IlluminaBlindspot_Regions(), "farhat_rlc": FarhatLab_RLC_Regions(), "farhat_rlc_lowmap": FarhatLab_RLC_LowMap_Regions(), "mtbseq": MTBseqRegions(),