parse_pon: Parse panel of normal variants to standardise output across...

In annaquaglieri16/samplepower: Compute sensitivity and false positive rates for a variant call set with repsect to a truth dataset.

Description

Parse panel of normal variants to standardise output across callers

Usage

parse_pon(path_to_pon, caller)

Arguments

path_to_pon	link to panel of normal file created with GATK3 VariantsToTable using at least
caller	one of 'varscan', 'mutect' or 'vardict'. This field is needed to parse the variant allele frequency field which is recorded differently across callers.

Examples

path_to_pon = "varscan_calls/PON_varscan_target_regions.table"

parse_varscan <- parse_pon(path_to_pon,'varscan')

annaquaglieri16/samplepower documentation built on Nov. 7, 2019, 11:43 p.m.