WISARD[wɪzərd] Workbench for Integrated Superfast Association study with Related Data |
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WISARD provides some useful functions for summarization of gene-level from dataset.
Regardless of gene-variant definition, actually mapped gene-variant definition can vary on the dataset. In order to identify which variants are actually mapped onto the gene from given dataset, --genesummary can be used.
Above command generates [prefix].summary.gene.lst, with below format.
summary.gene.lst is... | A summary of analyzed gene-variant information (TSV) | ||
Column | Format | Modifier | Description | CHR | non-negative real | NONE | Variance of entire sig | NAME | string | NONE | Retrieved gene name | COUNT | non-negative integer | NONE | Existing number of variants in the dataset for gene name | START | non-negative integer | NONE | Minimum position of variant belongs to gene | END | non-negative integer | NONE | Maximum position of variant belongs to gene | LIST | string | --verbose | List of variants belongs to gene |
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After the identification of significant genes associated with given dichotomous trait using given dataset and gene-variant definition, a further investigation on the allele frequency of variants in the genes can be performed. WISARD provides this function with --gmapsummary option.
NOTE! |
An assignment of single dichotomous phenotype is required to use this option! |
Above command generates [prefix].summary.gmap.lst, with below format.
summary.gmap.lst is... | A summary of variant distribution across case-control samples for each gene mapping (TSV) | ||
Column | Format | Modifier | Description | CHR | string | --verbose | List of variants belongs to gene | NAME | string | NONE | Retrieved gene name | VARIANT | string | NONE | Variant name belongs to gene | MINOR | string | NONE | Minor allele of variant | CASE0 | non-negative integer | NONE | Number of case samples having major homozygote | CASE1 | non-negative integer | NONE | Number of case samples having heterozygote | CASE2 | non-negative integer | NONE | Number of case samples having minor homozygote | CTRL0 | non-negative integer | NONE | Number of control samples having major homozygote | CTRL1 | non-negative integer | NONE | Number of control samples having heterozygote | CTRL2 | non-negative integer | NONE | Number of control samples having minor homozygote |
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Since above command investigates for all of genes in the gene-variant definition, it could be a huge task to be done. Thus it might be inefficient when the small portion of genes are interested. --selgene can be used for this situation.
Using only the portion of gene-variant definition to the analyses is also possible in WISARD. Below options are available.
One of most intuitive filtering can be applied on the genes is the number of included variants on the gene. It can be done with --genesize option.
NOTE! |
This option requires range type parameter! |
Although WISARD provides several options for filtering variant with genotype calling rate, gene-level calling rate can be considered. To use gene-level calling rate filtering, use --genemiss option.