write_vcf: write_vcf

In mskilab/skidb: Collection of R functions for accessing and parsing flat file dumps of common databases and external software used by @mskilab.

write_vcf

Description

writes any GRanges vars into vcf using columns of vars to guide choice of common fields like $FILTER $GT $REF $ALT

and adding all other fields to INFO

writes any GRanges vars into vcf using columns of vars to guide choice of common fields like $FILTER $GT $REF $ALT

and adding all other fields to INFO

Usage

write_vcf(
  vars,
  filename,
  sname = "mysample",
  info.fields = setdiff(names(values(vars)), c("FILTER", "GT", "REF", "ALT"))
)

write_vcf(
  vars,
  filename,
  sname = "mysample",
  info.fields = setdiff(names(values(vars)), c("FILTER", "GT", "REF", "ALT"))
)

Arguments

vars	info info
filename	string Path to output VCF
sname	string Sample name (defautl = 'mysample')
info.fields	info info

Author(s)

Marcin Imielinski

Marcin Imielinski

mskilab/skidb documentation built on Feb. 6, 2023, 2:49 a.m.