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

bam

meta:map

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

]

${prefix}.bam:file

Sorted BAM file

*.{bam}

cram

meta:map

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

]

${prefix}.cram:file

Sorted CRAM file

*.{cram}

sam

meta:map

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

]

${prefix}.sam:file

Sorted SAM file

*.{sam}

versions

versions.yml:file

File containing software versions

versions.yml

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
included in
raredisease variantcatalogue
maintainer
Github user ramprasadn
get in touch
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