Description

Left align and trim variants using GATK4 LeftAlignAndTrimVariants.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

The vcf file to be normalized e.g. ‘file1.vcf.gz’

tbi{:bash}

:file

Index of the vcf file to be normalized e.g. ‘file1.vcf.gz.tbi’

intervals{:bash}

:file

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

fasta{:bash}

:file

The reference fasta file

*.fasta

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

dict{:bash}

:file

GATK sequence dictionary

*.dict

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

VCF normalized output file

*.{vcf.gz}

tbi{:bash}

meta{:bash}

:map

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

*.tbi{:bash}

:file

Tbi index for VCF file

*.tbi

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
variantcatalogue
maintainer
Github user adamrtalbot
get in touch
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