Description

Use deamination patterns to estimate contamination in single-stranded libraries

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM/SAM file (Mandatory)

*.{bam,cram,sam}

meta2{:bash}

:map

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

config{:bash}

:file

Optional AuthentiCT configuration text file

*

meta3{:bash}

:map

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

positions{:bash}

:file

Optional text file with positions that sequences should overlap

*

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Maximum likelihood estimates with associated standard errors

*.txt

versions_authentict{:bash}

${task.process}{:bash}

:string

The name of the process

authentict{:bash}

:string

The name of the tool

echo \$(AuthentiCT --version 2>&1){:bash}

:eval

The expression to obtain the version of the tool

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'{: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

authentict{:bash}

:string

The name of the tool

echo \$(AuthentiCT --version 2>&1){:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

authentict
GPL v3

Estimates present-day DNA contamination in ancient DNA single-stranded libraries.

github.com/StephanePeyregne/AuthentiCT 10.1186/s13059-020-02123-y
maintainers
Github user scarlhoff
Github user StephanePeyregne
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