gemini_test_wrapper: GEMINI test (sub command) wrapper

In davemcg/SeeGEM: Integrate 'GEMINI' (and 'peddy') Output into Interactive Html Document

Description

Calls GEMINI's built in tools (e.g. autosomal_dominant, comp_hets) to retrieve proband/trio specific variants. Returns a tibble of all of the columns available in your GEMINI database.

Usage

gemini_test_wrapper(gemini_db, test = "autosomal_recessive",
  filter = paste("aaf < 0.1 AND aaf_esp_all < 0.01 AND",
  "aaf_1kg_all < 0.01 AND af_exac_all < 0.01 AND",
  "(is_coding=1 OR is_splicing=1 OR impact_severity='HIGH')",
  "AND filter is NULL"), min_gq = 20, families = NA, ...)

Arguments

gemini_db	is the name of your GEMINI database (with path, if necessary)
test	is the name of the GEMINI sub command to call. Accepted tests are autosomal_dominant, autosomal_recessive, comp_hets, mendel_errors, x_linked_de_novo, x_linked_dominant, x_linked_recessive. Use gemini_query_wrapper if you want to run a 'gemini query -q' style command.
filter	if you want to change the default filtering criteria
min_gq	minimum genotype quality (default is set at 20)
families	family name that GEMINI will use to identify proband, mother, and father
...	add other GEMINI commands not listed here

Value

None

Examples

## Not run: 
gemini_test_wrapper('/path/to/your/gemini.db', 'autosomal_dominant', 
families = 'fam007')

## End(Not run)

davemcg/SeeGEM documentation built on May 5, 2019, 1:34 a.m.