get_read_counts: Gets read counts for a specific locus in the genome

Description Usage Arguments Value

View source: R/get_read_counts.R

Description

Uses samtools pileup to get the read counts for each base in the genomic position specified

Usage

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get_read_counts(chr, pos, bam, tag = "", min_base_quality = 20,
  max_depth = 1e+05, min_mapq = 30)

Arguments

chr

chromosome name

pos

genomic coordinate

bam

path to bam file

tag

the RG tag if the bam has more than one sample

min_base_quality

minimum base quality for a read to be counted

max_depth

maximum depth above which sampling will happen

min_mapq

the minimum mapping quality for a read to be counted

Value

a list, number of reads for each of the four basepairs


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