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

]

bam (file)

BAM file

*.bam

meta2 (map)

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

]

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

meta (map)

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

]

bam (file)

Filtered consensus BAM file

*.bam

versions (file)

File containing software versions

versions.yml
maintainer
Github user lescai
get in touch
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