Description

Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file

*.bam

meta2{:bash}

:map

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

fasta{:bash}

:file

Fasta file containing genomic sequence information

*.{fa,fasta,fna}

index{:bash}

:file

Fasta index file

*.fai

dict{:bash}

:file

Fasta dictionary file

*.dict

min_reads{:bash}

:integer

Minimum number of reads required to keep a consensus read

min_baseq{:bash}

:file

Minimum base quality to consider

max_base_error_rate{:bash}

:file

Maximum base error rate for a position before it is replaced with an N.

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

${prefix}.bam{:bash}

:file

Filtered consensus BAM file

*.bam

versions_fgbio{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fgbio{:bash}

:string

The tool name

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fgbio{:bash}

:string

The tool name

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
radseq
maintainer
Github user lescai
get in touch
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