grok_bcf: Reads and parses bcf via bcftools call

In mskilab/skitools: Various mskilab R utilties

Reads and parses bcf via bcftools call

Description

Reads and parses bcf via bcftools call

Usage

grok_bcf(
  bcf,
  gr = NULL,
  bpath = "/nfs/sw/bcftools/bcftools-1.9/bin/bcftools",
  label = NA,
  filter = "PASS",
  snv = FALSE,
  indel = FALSE,
  het = FALSE,
  hom = FALSE,
  keep.modifier = TRUE,
  long = FALSE,
  oneliner = FALSE,
  verbose = FALSE
)

Arguments

bcf	path to bcf file
gr	optional granges to query
bpath	path to bcftools binary executable

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.