merge_bam_files: Merge multiple BAM files to a single output BAM file

In AllenInstitute/lowcat: Low Coverage Accessibility and Transcriptomics

Description

Merge multiple BAM files to a single output BAM file

Usage

merge_bam_files(bam_files, out_file, make_indexes = FALSE,
  sort_out_file = TRUE, index_out_file = TRUE, keep_unsorted = FALSE)

Arguments

bam_files	a character vector listing all of the BAM files to merge
out_file	the target BAM file to write to
make_indexes	whether or not to make indexes for the input files. Default is FALSE
sort_out_file	whether or not to sort the output file. default is TRUE, which will force index_out_file to TRUE.
index_out_file	whether or not to index the output file. Default is TRUE.
keep_unsorted	If sort_out_file == TRUE, whether or not to keep the original, unsorted file. Default is FALSE.

AllenInstitute/lowcat documentation built on Oct. 30, 2019, 4:45 a.m.