Description

Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps

*.vcf.gz

meta2{:bash}

:map

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

vcf_indels{:bash}

:file

Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels

*.vcf.gz

meta3{:bash}

:map

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

reference{:bash}

:file

Fasta file of reference genome

*.fasta

meta4{:bash}

:map

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

fai{:bash}

:file

Optional index for the fasta file of reference genome

*.fai

vcf_output{:bash}

:boolean

Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced

Output

name:type
description
pattern

fasta{:bash}

meta{:bash}

:map

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

*.fasta.gz{:bash}

:file

Gzipped consensus fasta file with bases under threshold replaced with Ns

*.fasta.gz

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns

*.vcf.gz

ccf{:bash}

meta{:bash}

:map

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

*.ccf{:bash}

:file

Statistics file containing information about the consensus calls in the fasta file

*.ccf

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

Log file

*.log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

topas
CC-BY

This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules.

github.com/subwaystation/TOPAS github.com/subwaystation/TOPAS/wiki/Overview-Modules https://github.com/subwaystation/TOPAS 10.1038/s41598-017-17723-1
maintainer
Github user aidaanva
get in touch
Ask a question on Slack Open an issue on GitHub