vcf2mvrl: Convert a VCF to an MVRangesList object

In trichelab/MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

Convert a VCF to an MVRangesList object

Usage

vcf2mvrl(
  vcf_filename,
  bam_filename = NULL,
  gzip = TRUE,
  biscuit = FALSE,
  verbose = TRUE
)

Arguments

vcf_filename	A filename/path to the corresponding VCF
bam_filename	A filename/path to the corresponding BAM
gzip	Is the input gzipped? (TRUE; really ought not matter)
biscuit	Is the input VCF from biscuit? (FALSE)
verbose	Print all messages during progress? (TRUE)

Value

an MVRangesList

Examples

library(MTseekerData)
VCFdir <- system.file("extdata", package="MTseekerData")
VCF <- file.path(VCFdir, list.files(VCFdir, pattern="*.vcf.gz$"))
mvr <- vcf2mvrl(VCF)[[1]]
mvr$FILTER <- ifelse(totalDepth(mvr) >= 20, "PASS", ".")
mvr$PASS <- mvr$FILTER == "PASS"
filterMT(mvr)

trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.