Description

This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.

Input

name:type
description
pattern

fasta

:file

FASTA reference file

*.{fasta,fa}

fasta_fai

:file

index of the FASTA reference file

*.fai

dict

:file

Sequence dictionary of the FASTA reference file

*.dict

Output

name:type
description
pattern

str_table

*.zip

:file

A zipped folder containing the STR table files

*.zip

versions_gatk4

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

:eval

The expression to obtain the version of the tool

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/articles/4405451249819-ComposeSTRTableFile 10.1158/1538-7445.AM2017-3590
maintainer
Github user nvnieuwk
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