Description Usage Arguments Examples
Convert paired-end bam files to fastqs and then realign with bwa mem
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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"
)
|
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'. |
1 2 3 4 5 6 7 8 9 10 | ## 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)
|
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