get_pos: A function to get the positions of the reads given a BAM file
In malemay/delgbs: Detection of deletions and duplications from GBS data

get_pos

R Documentation

A function to get the positions of the reads given a BAM file

Description

Outputs a data.frame containing the chromosome, initial base position, and mapping quality for every read in the data set. Filters based on mapping quality (default = 30, but different thresholds should be tested).

Usage

get_pos(filename, minq = 30, strand_diff = FALSE)

Arguments

`filename`	character, the name of the bam file
`minq`	integer, the minimum mapping quality for a read to be kept
`strand_diff`	a logical of length 1 (`TRUE` or `FALSE`). If `TRUE`, reads mapping to the "+" strand are tallied according to their 3'-most position, whereas reads mapping to the "-" strand are tallied according to their 5'-most position. If `FALSE`, all reads are tallied according to their 5'-most position. This option should be chosen according to the expected mean size of the restriction fragments, so as to maximize the probability that two reads originating from the same restriction fragment but with differing orientation are counted in the same bin.