Description

Create a fasta with the bases shifted by offset

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

fasta file

*.{fa,fasta}

meta2{:bash}

:map

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

fasta_fai{:bash}

:file

index for fasta file

*.{fai}

meta3{:bash}

:map

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

dict{:bash}

:file

sequence dictionary file

*.{dict}

Output

name:type
description
pattern

shift_fa{:bash}

meta{:bash}

:map

Groovy Map containing fasta information e.g. [ id:‘test’ ]

*_shift.fasta{:bash}

:file

Shifted fasta file

*.{fa,fasta}

shift_fai{:bash}

meta{:bash}

:map

Groovy Map containing fasta information e.g. [ id:‘test’ ]

*_shift.fasta.fai{:bash}

:file

Index file for the shifted fasta file

*.{fai}

shift_back_chain{:bash}

meta{:bash}

:map

Groovy Map containing fasta information e.g. [ id:‘test’ ]

*_shift.back_chain{:bash}

:file

The shiftback chain file to use when lifting over

*.{back_chain}

dict{:bash}

meta{:bash}

:map

Groovy Map containing fasta information e.g. [ id:‘test’ ]

*_shift.dict{:bash}

:file

sequence dictionary file

*.{dict}

intervals{:bash}

meta{:bash}

:map

Groovy Map containing fasta information e.g. [ id:‘test’ ]

*.intervals{:bash}

:file

Intervals file for the fasta file

*.{intervals}

shift_intervals{:bash}

meta{:bash}

:map

Groovy Map containing fasta information e.g. [ id:‘test’ ]

*.shifted.intervals{:bash}

:file

Intervals file for the shifted fasta file

*.{shifted.intervals}

versions_gatk4{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

: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/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
included in
raredisease
maintainer
Github user ramprasadn
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