Description

Converts BAM/SAM file to FastQ format

Input

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

Input SAM/BAM file

*.{bam,sam}

Output

Name (Type)
Description
Pattern

fastq (file)

converted fastq file

*.fastq

versions (file)

File containing software versions

versions.yml
included in
raredisease variantcatalogue
author
Github user kevinmenden
get in touch
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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