Man pages for quevedor2/WadingPool
A toolkit for shallow/low-pass whole genome sequencing analysis
| aggregateAndFilter | Aggregate samples and filter SNPs |
| allbyall | rowxrow or colxcol execution |
| calcExpectedHets | Calculates expected number of heterozygous SNPs |
| combZygPos | Zygosity combiner helper |
| fitHMM | Fit an HMM |
| genSnpZygosity | Simplifies the SNP Zygosity from MuTect |
| getExpectedN | Calculates the expected number of SNPs |
| getSampleSimilarity | Generates a similarity matrix |
| metrics | Multi-class performance metrics |
| parseOutput | Returns the tag from an execution |
| parseSeg | Parse CN seg files |
| plotCnZyg | Cn-Zyg plotter |
| plotHMM | Plot zygosity HMM |
| plotSampleSimilarity | Sim-N plotter |
| sanitizeData | Sanitize the data |
| saturationCurve | Saturation curve estimations using asymptotic regression... |
| simulate | simulate |
| toBed | GRanges to Bed |
