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 (map)

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

]

vcf (file)

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

*.vcf.gz

vcf_indels (file)

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

*.vcf.gz

reference (file)

Fasta file of reference genome

*.fasta

fai (file)

Optional index for the fasta file of reference genome

*.fai

vcf_output (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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

fasta (file)

Gzipped consensus fasta file with bases under threshold replaced with Ns

*.fasta.gz

vcf (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 (file)

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

*.ccf

log (file)

Log file

*.log
mantainer
Github user aidaanva
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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/TOPAS10.1038/s41598-017-17723-1