Description

Create a fasta with the bases shifted by offset

Input

Name (Type)
Description
Pattern

meta (map)

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

fasta (file)

fasta file

*.{fa,fasta}

meta2 (map)

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

fasta_fai (file)

index for fasta file

*.{fai}

meta3 (map)

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

dict (file)

sequence dictionary file

*.{dict}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

dict (file)

sequence dictionary file

*.{dict}

intervals (file)

Intervals file for the fasta file

*.{intervals}

shift_back_chain (file)

The shiftback chain file to use when lifting over

*.{back_chain}

shift_fa (file)

Shifted fasta file

*.{fa,fasta}

shift_intervals (file)

Intervals file for the shifted fasta file

*.{shifted.intervals}
included in
raredisease
maintainer
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub

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