read_manta_vcf: Read Manta VCF

In pdiakumis/rock: Rocking R at UMCCR

Description

Read main columns of interest from Manta VCF using bcftools or bedr

Usage

read_manta_vcf(vcf)

Arguments

vcf	Path to Manta VCF file (.vcf.gz or .vcf).

Details

Uses bcftools (https://samtools.github.io/bcftools/bcftools.html) or bedr (https://cran.r-project.org/web/packages/bedr/index.html) to read in the VCF file.

Value

A dataframe (tibble) with the following fields from the VCF:

• chrom1: CHROM (remove chr prefix (if any) for hg38 compatibility)

• pos1: POS | INFO/BPI_START

• pos2: INFO/END | INFO/BPI_END

• id: ID

• mateid: INFO/MATEID

• svtype: INFO/SVTYPE

• filter: FILTER

Examples

vcf <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
vcf2 <- system.file("extdata", "manta_no_bpi.vcf", package = "pebbles")
rock:::read_manta_vcf(vcf)
rock:::read_manta_vcf(vcf2)

pdiakumis/rock documentation built on Oct. 12, 2020, 9:38 a.m.