Description

Call somatic SNVs and indels via local assembly of haplotypes.

Input

Name (Type)
Description
Pattern

meta (map)

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

input (list)

list of BAM files, also able to take CRAM as an input

*.{bam/cram}

input_index (list)

list of BAM file indexes, also able to take CRAM indexes as an input

*.{bam.bai/cram.crai}

intervals (file)

Specify region the tools is run on.

.{bed,interval_list}

meta2 (map)

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

fasta (file)

The reference fasta file

*.fasta

meta3 (map)

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

fai (file)

Index of reference fasta file

*.fasta.fai

meta4 (map)

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

dict (file)

GATK sequence dictionary

*.dict

germline_resource (file)

Population vcf of germline sequencing, containing allele fractions.

*.vcf.gz

germline_resource_tbi (file)

Index file for the germline resource.

*.vcf.gz.tbi

panel_of_normals (file)

vcf file to be used as a panel of normals.

*.vcf.gz

panel_of_normals_tbi (file)

Index for the panel of normals.

*.vcf.gz.tbi

Output

Name (Type)
Description
Pattern

vcf (file)

compressed vcf file

*.vcf.gz

tbi (file)

Index of vcf file

*vcf.gz.tbi

stats (file)

Stats file that pairs with output vcf file

*vcf.gz.stats

f1r2 (file)

file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)

*.f1r2.tar.gz

versions (file)

File containing software versions

versions.yml
included in
createpanelrefs raredisease rnadnavar sarek variantcatalogue
maintainers
Github user GCJMackenzie
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