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GEMINI burden (version 0.10.1.0)

GEMINI database:

Only files with version 0.10.1 are accepted.

Space separated list of cases for association testing:

(--cases)

Space separated list of controls for association testing:

(--controls)

Save the permuted T-scores in the output file:

(--save_tscores)

Count all nonsynonymous variants as contributing burden:

(--nonsynonymous)

Run the C-alpha association test:

(--calpha)

The min. alt. allele frequency for a variant to be included:

(--min-aaf)

The max. alt. allele frequency for a variant to be included:

(--max-aaf)

Number of permutations to run for the C-alpha test:

(--permutations)

What it does

The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample.

$ gemini burden test.burden.db gene M10475 M10478 M10500 M128215 WDR37 2 2 2 2 CTBP2 0 0 0 1 DHODH 1 0 0 0

Citation

If you use GEMINI in your research, please cite the following manuscript: