Description

Lofreq subcommand to for insert base and indel alignment qualities

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

bam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

fasta (file)

Reference genome FASTA file

*.{fasta}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

bam (file)

BAM/CRAM/SAM file with base and indel alignment qualities

*.{bam,cram,sam}
maintainer
Github user MarieLataretu
get in touch
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Tools

lofreq
MIT

A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data

csb5.github.io/lofreq csb5.github.io/lofreq/commands 10.1093/nar/gks918