pealignBwa: pealignBwa

Description Usage Arguments Examples

View source: R/pealignBwa.R

Description

Align paired-end fq files using bwa mem

Usage

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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

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## 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.