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Modlin ibs #3

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69b5f8e
Add list of regions identified as illumina blind spots in www.ncbi.nl…
biominer Feb 15, 2023
ed8c674
Document addition of Modlin et al. Illumina Blindspots region list fo…
biominer Feb 15, 2023
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11 changes: 6 additions & 5 deletions README.md
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Expand Up @@ -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. Mask out variants with less than a minimum percentage
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