Description

Call germline SNPs and indels via local re-assembly of haplotypes

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file from alignment

*.{bam,cram}

input_index{:bash}

:file

BAI/CRAI file from alignment

*.{bai,crai}

intervals{:bash}

:file

Bed file with the genomic regions included in the library (optional)

dragstr_model{:bash}

:file

Text file containing the DragSTR model of the used BAM/CRAM file (optional)

*.txt

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

fasta.fai

meta4{:bash}

:map

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

dict{:bash}

:file

GATK sequence dictionary

*.dict

meta5{:bash}

:map

Groovy Map containing dbsnp information e.g. [ id:‘test_dbsnp’ ]

dbsnp{:bash}

:file

VCF file containing known sites (optional)

meta6{:bash}

:map

Groovy Map containing dbsnp information e.g. [ id:‘test_dbsnp’ ]

dbsnp_tbi{:bash}

:file

VCF index of dbsnp (optional)

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

Compressed VCF file

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.tbi{:bash}

:file

Index of VCF file

*.vcf.gz.tbi

bam{:bash}

meta{:bash}

:map

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

*.realigned.bam{:bash}

:file

Assembled haplotypes and locally realigned reads

*.realigned.bam

versions{:bash}

versions.yml{:bash}

: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
pacvarrnavarsarek
maintainers
Github user suzannejin
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub