calmdBam: Calculate MD tag for BAM
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

calmdBam

R Documentation

Calculate MD tag for BAM

Description

Add the MD tag to BAM file and replace matches with “=” in ‘seq’.

Usage

  calmdBam(bamFns, genomeFn, mc.cores=4L)

Arguments

`bamFns`	`character`(n): filenames of BAM files.
`genomeFn`	`character`(1): the reference fasta file for the alignment.
`mc.cores`	`integer`(1): the number of cores to use.

Details

It uses the “calmd” from samtools.

Value

Filenames of returned BAM files.

Examples

  bamFns <- list.files("/scratch/gtan/R2ErrorRates/GEORNASeqBam",
                       pattern="\\.bam$", recursive = TRUE, full.names = TRUE)
  calmdBam(bamFns, 
           genomeFn="/scratch/gtan/R2ErrorRates/reference/Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26/Genes/BOWTIE2Index/transcripts.fa")

uzh/ezRun documentation built on Sept. 16, 2024, 11:21 p.m.