Description

Print reads in the SAM/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/SAM file

*.{bam,cram,sam}

index (file)

BAM/CRAM/SAM file

*.{bai,crai,sai}

meta2 (map)

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

fasta (file)

reference fasta file

*.{fa,fasta}

meta3 (map)

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

fai (file)

reference fasta index file

*.{fai}

meta4 (map)

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

dict (file)

reference fasta dictionary file

*.{dict}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

Sorted BAM file

*.{bam}

cram (file)

Sorted CRAM file

*.{cram}

sam (file)

Sorted SAM file

*.{sam}
included in
raredisease variantcatalogue
maintainer
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590