WISARD[wɪzərd] Workbench for Integrated Superfast Association study with Related Data |
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Mendelian error can be evaluated for family-based samples and WISARD provides a simple function to calculate Mendelian error rates by using --mendel option.
Running WISARD with --mendel option produces three output files: [prefix].family.res, [prefix].sample.res and [prefix].variant.res.
Columns in each output file have a different meaning as follows:
mendel.family.res is... | A result of analysis of family-wise Mendelian transmission error (TSV) | ||
Column | Format | Modifier | Description | FID | string | NONE | Family ID of Mendelian error investigated | ERROR | integer | NONE | Number of alleles have Mendelian error for the family | AVAIL | integer | NONE | Number of called alleles for the family | PROP | real | NONE | Mendelian error rate for the family |
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mendel.sample.res is... | A result of analysis of sample-wise Mendelian transmission error (TSV) | ||
Column | Format | Modifier | Description | FID | string | NONE | Family ID of the sample of Mendelian error investigated | IID | string | NONE | Individual ID of Mendelian error investigated | ERROR | integer | NONE | Number of alleles have Mendelian error for the sample | AVAIL | integer | NONE | Number of called alleles for the sample | PROP | real | NONE | Mendelian error rate for the sample |
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mendel.variant.res is... | A result of analysis of variant-wise Mendelian transmission error (TSV) | ||
Column | Format | Modifier | Description | CHR | real | NONE | Mendelian error rate for the sample | VARIANT | real | NONE | Mendelian error rate for the sample | POS | real | NONE | Mendelian error rate for the sample | ALT | real | NONE | Mendelian error rate for the sample | ANNOT | real | NONE | Mendelian error rate for the sample | ERROR | integer | NONE | Number of alleles have Mendelian error for the variant | AVAIL | integer | NONE | Number of called alleles for the variant | PROP | real | NONE | Mendelian error rate for the variant |
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It filters sample(s) samples or families by the portion of genotypes having Mendelian transmission error.
NOTE! |
The parameter of this option supports range type parameter |
NOTE! |
The parameter of this option supports range type parameter |