modules/lofreq_viterbi

Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available

variant callinglow frequency variant callingvariantsbamprobabilistic realignment

https://github.com/nf-core/modules/[...]/modules/nf-core/lofreq/viterbi

Description

Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Sorted BAM file

*.{bam}

`meta2`
`:map`

Groovy Map containing sample information about the reference fasta e.g. [ id:‘reference’ ]

`fasta`
`:file`

Reference genome FASTA file

*.{fasta}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Realignment and sorted BAM file

*.{bam}

`versions_lofreq`

`${task.process}`
`:string`

Process which generated the version

`lofreq`
`:string`

Tool name

`lofreq version | sed -n '1s/^.* //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

Process which generated the version

`lofreq`
`:string`

Tool name

`lofreq version | sed -n '1s/^.* //p'`
`:eval`

The expression to obtain the version of the tool

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

modules/lofreq_viterbi

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_lofreq`

`${task.process}`
`:string`

`lofreq`
`:string`

`lofreq version | sed -n '1s/^.* //p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`lofreq`
`:string`

`lofreq version | sed -n '1s/^.* //p'`
`:eval`

Tools

lofreq
MIT

maintainers

get in touch

modules/lofreq_viterbi

Description

Input

meta :map

bam :file

meta2 :map

fasta :file

Output

bam

meta :map

*.bam :file

versions_lofreq

${task.process} :string

lofreq :string

lofreq version | sed -n '1s/^.* //p' :eval

Topics

versions

${task.process} :string

lofreq :string

lofreq version | sed -n '1s/^.* //p' :eval

Tools

lofreqMIT

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_lofreq`

`${task.process}`
`:string`

`lofreq`
`:string`

`lofreq version | sed -n '1s/^.* //p'`
`:eval`

`versions`

`${task.process}`
`:string`

`lofreq`
`:string`

`lofreq version | sed -n '1s/^.* //p'`
`:eval`

lofreq
MIT