filterVcf: Filter vcf for compatibility with downstream functions

Description Usage Arguments Value

View source: R/preProcessSnvIndel.R

Description

Wrapper function for SnpSift filter and SnpSift intervals. Selects PASS variants and variants at coords specified in bed file. For germline vcfs, remove somatic variants.

Usage

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filterVcf(
  vcf.file,
  out.file,
  mode = NULL,
  bed.file = BED_FILE,
  java.path = JAVA_PATH,
  snpsift.path = SNPSIFT_PATH
)

Arguments

vcf.file

Path to vcf file (gzip compressed)

out.file

Path to output vcf file (make sure to add .gz at the end)

mode

Can be 'germ' or 'som'

bed.file

Path to bed file specifying the genome intervals to keep (defaults ot the one stored in this package)

java.path

Path to java binary (defaults to the installed JRE location)

snpsift.path

Path to SnpSift jar (defaults to the one included in this package)

Value

Nothing but writes a gzipped vcf file


luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.