realignBwa: realignBwa

Description Usage Arguments Examples

View source: R/realignBwa.R

Description

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

Usage

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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

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## 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.