pealignBwa: pealignBwa

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

Description

Align paired-end fq files using bwa mem

Usage

pealignBwa(
  fq1,
  fq2,
 
    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"
)

Arguments

fq1	Fastq R1 file of paired-end data.
fq2	Fastq R2 file of paired-end data.
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'.

Examples

## Not run: 
fq1 <- '/media/msubirana/insulinomas/epimutations/processed/hg37/bam/longranges/wgs/sub_10759_R1.fa'
fq2 <- '/media/msubirana/insulinomas/epimutations/processed/hg37/bam/longranges/wgs/sub_10759_R2.fa'
ref <- '/home/msubirana/Documents/phd/refgen/hg38/hg38.fa'
out_dir <- '/media/msubirana/insulinomas/epimutations/processed/hg37/bam/longranges/wgs/subset_proves'
threads <- 6
pealignBwa(fq1=fq1,
           fq2=fq2,
           ref=ref,
           out_dir=out_dir)

## End(Not run)

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