bwa/bwa_sampe

alignment

BWA

BWA-sampe

SAM

paired-end

Description

BWA sampe - generate paired-end alignment in SAM format from BWA aln SAI files.

Type

bash_script

License

MIT

Keywords

alignment

BWA

BWA-sampe

SAM

paired-end

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.sam"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bwa/bwa_sampe/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--index	file required	BWA index base name (prefix of .amb, .ann, .bwt, .pac, .sa files).
--sai1	file required	Input SAI file for first reads (R1) generated by BWA aln.
--sai2	file required	Input SAI file for second reads (R2) generated by BWA aln.
--reads1	file required	Input FASTQ file with first reads in pair (R1).
--reads2	file required	Input FASTQ file with second reads in pair (R2).

Name

Type & Properties

--index

file

required

--sai1

file

required

--sai2

file

required

--reads1

file

required

--reads2

file

required

Output

Name	Type & Properties	Description
--output -f	file output	Output SAM file. If not specified, output goes to stdout.

Name

Type & Properties

--output

-f

file

output

Pairing Options

Name	Type & Properties	Description
--max_insert_size -a	integer	Maximum insert size. Default is 500.
--max_occ_one_end -o	integer	Maximum occurrences for one end. Default is 100000.
--max_hits_paired -n	integer	Maximum hits to output for paired reads. Default is 3.
--max_hits_discordant -N	integer	Maximum hits to output for discordant pairs. Default is 10.
--chimeric_rate -c	double	Prior of chimeric rate (lower bound). Default is 1.0e-05.

Name

Type & Properties

--max_insert_size

-a

integer

--max_occ_one_end

-o

integer

--max_hits_paired

-n

integer

--max_hits_discordant

-N

integer

--chimeric_rate

-c

double

Algorithm Options

Name	Type & Properties	Description
--read_group -r	string	Read group header line such as '@RG\tID:foo\tSM:bar'.
--preload_index -P	boolean_true	Preload index into memory (for base-space reads only).
--disable_smith_waterman -s	boolean_true	Disable Smith-Waterman for the unmapped mate.
--disable_insert_size_estimate -A	boolean_true	Disable insert size estimate (force -s).

Name

Type & Properties

--read_group

-r

string

--preload_index

-P

boolean_true

--disable_smith_waterman

-s

boolean_true

--disable_insert_size_estimate

-A

boolean_true