get_mutation_read_names: Gets names of the reads showing reference and alternative...

Description Usage Arguments Value

View source: R/get_mutation_read_names.R

Description

Extract the names of the reads in a bam file that support the variant allele of a single mutation

Usage

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get_mutation_read_names(bam, chr, pos, ref, alt, tag = "",
  min_base_quality = 20, min_mapq = 30)

Arguments

bam

path to bam file.

chr

Chromosome name for the mutation.

pos

Chromosome position for the mutation.

ref

The reference allele of the mutation.

alt

The alternative allele of the mutation.

tag

the RG tag if the bam has more than one sample.

min_base_quality

integer specifying the minimum base quality for reads to be included.

min_mapq

integer specifying the minimum mapping quality for reads to be included.

Value

A character vector having the read names


ctDNAtools documentation built on March 26, 2020, 7:39 p.m.