Description

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

Input

name:type
description
pattern

meta:map

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

bam:file

BAM file

*.bam

meta2:map

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

fasta:file

Fasta file containing genomic sequence information

*.bam

min_reads:integer

Minimum number of reads required to keep a consensus read

min_baseq:file

Minimum base quality to consider

max_base_error_rate:file

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

Output

name:type
description
pattern

bam

meta:map

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

${prefix}.bam:file

Filtered consensus BAM file

*.bam

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
radseq
maintainer
Github user lescai
get in touch
Ask a question on Slack Open an issue on GitHub