calmdBam: Calculate MD tag for BAM

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

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 Dec. 26, 2024, 9:53 a.m.