realignBwa: realignBwa

In msubirana/DNAseqPipeline: What the Package Does (One Line, Title Case)

Description

Convert paired-end bam files to fastqs and then realign with bwa mem

Usage

realignBwa(
  bam,
 
    ref = "/gpfs42/projects/lab_lpasquali/shared_data/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa",
  out_dir,
  threads = 1,
  temp = file.path(out_dir, "temp"),
  platform = "ILLUMINA",
  bwa = "bwa",
  samtools = "samtools",
  samblaster = "samblaster",
  gatk = "/gpfs42/projects/lab_lpasquali/shared_data/marc/repos/gatk-4.1.9.0/gatk"
)

Arguments

bam	Paired-end BAM file to realign
ref	Reference genome (ref.fa) to use for the alignment.
threads	Number of threads to use in the analysis.
platform	Platforme used in the sequecing process. By default 'ILLUMINA'.
bwa	Path to the executable bwa. By default 'bwa'.
samtools	Path to the executable bwa. By default 'samtools'.
samblaster	Path to the executable bwa. By default 'samblaster'.
gatk	Path to the executable gatk By default '/gpfs42/projects/lab_lpasquali/shared_data/marc/repos/gatk-4.1.9.0/gatk'.

Examples

## Not run: 
bam <- '/media/msubirana/insulinomas/epimutations/processed/hg37/bam/longranges/wgs/sub_10759.bam'
ref <- '/home/msubirana/Documents/phd/refgen/hg38/hg38.fa'
out_dir <- '/media/msubirana/insulinomas/epimutations/processed/hg37/bam/longranges/wgs/subset_proves'
threads <- 6
realignBwa(bam=bam,
           ref=ref,
           out_dir=out_dir)

## End(Not run)

msubirana/DNAseqPipeline documentation built on Dec. 21, 2021, 10:12 p.m.