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,fasta.gz}

meta3:map

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

fai:file

Index of reference fasta file

*.{fasta.fai,fasta.fai.gz}

gzi:file

Index of bgzipped reference fasta file

*.fasta.gz.gzi

meta4:map

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

dict:file

GATK sequence dictionary

*.dict

alleles:file

vcf file to be used to force-call alleles.

*.vcf.gz

alleles_tbi:file

Index file for alleles to be force-called.

*.vcf.gz.tbi

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

meta:map

A Groovy map containing sample information

*.vcf.gz:file

compressed vcf file

*.vcf.gz

tbi

meta:map

A Groovy map containing sample information

*.tbi:file

Index of vcf file

*vcf.gz.tbi

stats

meta:map

A Groovy map containing sample information

*.stats:file

Stats file that pairs with output vcf file

*vcf.gz.stats

f1r2

meta:map

A Groovy map containing sample information

*.f1r2.tar.gz:file

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

*.f1r2.tar.gz

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
createpanelrefsrarediseasernadnavarsarekvariantcatalogue
maintainers
Github user GCJMackenzie
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub