samtoolsMpileup: Calls the samtools 'mpileup' command

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Calls the samtools 'mpileup' command.

Usage

## Default S3 method:
samtoolsMpileup(refFile, bamFile, pathnameD="mpileup.out", ..., verbose=FALSE)

Arguments

refFile	input reference file
bamFile	input BAM file (currently only one file is supported)
pathnameD	output file (default 'mpileup.out')
...	Additional arguments specifying samtools 'mpileup' switches passed to systemSamtools().
verbose	See Verbose.

Author(s)

Taku Tokuyasu

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.