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WISARD[wɪzərd] Workbench for Integrated Superfast Association study with Related Data |
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This section describes about
Transitions (Ts) indicate pyrimidine-pyrimidine mutations (C <-> T) and purine-purine mutations (A <-> G).
Transversions (Tv) mean pyrimidine-pyrimidine mutation or vice persa.
C can easily get methylated and once it is methylated, it turns into U/T if it is deaminated.
In particular when C is adjacent to a G i.e. CpG and C turns into U/T, it causes G->A.
Therefore, transitions occur at a higher rate than transversions.
For human, the Ti/Tv ratio(also known as Ti/Tv) should be around 2.1 for whole genome sequencing and 2.8 for whole exome.
If it is lower, that means your data includes false positives caused by random sequencing errors
Ts/Tv ratio for given dataset is easily computed with WISARD by using "--tstv window-size" option.
window-size should be integer (basepairs).
Running this code produces two files, [prefix].tstv.variant.lst and [prefix].tstv.chr.lst.
Running WISARD with --tstv option produces the following [prefix].tstv.variant.lst:
| tstv.variant.lst is... | A result of Ts/Tv ratio by window (TSV) | ||
| Column | Format | Modifier | Description | CHR | 1~22/X/Y/Mt/Un | NONE | Target chromosome | SZBIN | integer | --tstv | Window size | SZCHR | integer | NONE | Maxially observed physical position in current chromosome | NBIN | integer | NONE | Number of generated bins in current chromosome | TSTV | real numbers divided by space | NONE | Ts/Tv ratio values |
|---|---|---|---|
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NOTE! |
Ts/Tv ratio computation is achievelable when genotypes in ped/bem/vef files are coded as A/C/G/T, and otherwise it cannot be calculated! |