Description

Merge BAM or CRAM file

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input_files (file)

BAM/CRAM file

*.{bam,cram,sam}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (file)

Reference file the CRAM was created with (optional)

*.{fasta,fa}

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fai (file)

Index of the reference file the CRAM was created with (optional)

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM file

*.{bam}

cram (file)

CRAM file

*.{cram}

versions (file)

File containing software versions

versions.yml

csi (file)

BAM index file (optional)

*.csi

crai (file)

CRAM index file (optional)

*.crai
included in
bamtofastq callingcards fastquorum hicar phaseimpute radseq raredisease rnadnavar rnavar sarek scnanoseq
maintainers
Github user drpatelh
Github user yuukiiwa
Github user maxulysse
Github user FriederikeHanssen
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352