Description

Left align and trim variants using GATK4 LeftAlignAndTrimVariants.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

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

tbi (file)

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

intervals (file)

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

fasta (file)

The reference fasta file

*.fasta

fai (file)

Index of reference fasta file

*.fasta.fai

dict (file)

GATK sequence dictionary

*.dict

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

VCF normalized output file

*.{vcf.gz}

tbi (file)

Tbi index for VCF file

*.tbi
included in
variantcatalogue
author
Github user adamrtalbot
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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