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Updated manual
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Lennart authored and Lennart committed Jan 5, 2021
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Expand Up @@ -103,7 +103,7 @@ WisecondorX predict test_input.npz reference_input.npz output_id [--optional arg
`--zscore x` | Z-score cutoff to call segments as aberrations (default: x=5)
`--alpha x` | P-value cutoff for calling circular binary segmentation breakpoints (default: x=1e-4)
`--beta x` | When beta is given, `--zscore` is ignored. Beta sets a ratio cutoff for aberration calling. It's a number between 0 (liberal) and 1 (conservative) and, when used, is optimally close to the purity (e.g. fetal/tumor fraction)
`--blacklist x` | Blacklist for masking additional regions; requires headerless .bed file. This is particularly useful when the reference set is too small to recognize some obvious loci (such as centromeres; example at `./example.blacklist/centromere.hg38.txt`)
`--blacklist x` | Blacklist for masking additional regions; requires headerless .bed file. This is particularly useful when the reference set is too small to recognize some obvious loci (such as centromeres; examples at `./example.blacklist/`)
`--gender x` | Force WisecondorX to analyze this case as male (M) or female (F). Useful when e.g. dealing with a loss of chromosome Y, which causes erroneous gender predictions (choices: x=F or x=M)
`--bed` | Outputs tab-delimited .bed files (trisomy 21 NIPT example at `./example.bed`), containing all necessary information **(\*)**
`--plot` | Outputs custom .png plots (trisomy 21 NIPT example at `./example.plot`), directly interpretable **(\*)**
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