Description

convert and then index CRAM -> BAM or BAM -> CRAM file

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM file

*.{bam,cram}

index (file)

BAM/CRAM index file

*.{bai,crai}

fasta (file)

Reference file to create the CRAM file

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

filtered/converted BAM file

*{.bam}

cram (file)

filtered/converted CRAM file

*{cram}

bai (file)

filtered/converted BAM index

*{.bai}

crai (file)

filtered/converted CRAM index

*{.crai}

version (file)

File containing software version

*.{version.txt}
included in
rnadnavar sarek
maintainers
Github user FriederikeHanssen
Github user maxulysse
Github user matthdsm
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