modules/pindel_pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data

deletionsinsertionstandem duplications

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

Description

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics or a sensible default - setting ext.args2 to either in modules.conf e.g. [ id:‘test’, single_end:false, insert_size:500 ]

`bam`
`:file`

BAM file

*.bam

`bai`
`:file`

BAM index file

*.bai

`fasta`
`:file`

Input reference genome fasta file

`fai`
`:file`

Input reference genome fasta index file

`bed`
`:file`

BED file containing regions of interest

Output

name:type

description

pattern

`bp`

`meta`
`:map`

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

`*_BP`
`:file`

File containing breakpoints

*_{BP}

`cem`

`meta`
`:map`

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

`*_CloseEndMapped`
`:file`

File containing close end reads

*_{CloseEndMapped}

`del`

`meta`
`:map`

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

`*_D`
`:file`

File containing deletions

*_{D}

`dd`

`meta`
`:map`

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

`*_DD`
`:file`

File containing dispersed duplications

*_{DD}

`int_final`

`meta`
`:map`

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

`*_INT_final`
`:file`

int file

*_INT_final

`inv`

`meta`
`:map`

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

`*_INV`
`:file`

File containing inversions

*_{INV}

`li`

`meta`
`:map`

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

`*_LI`
`:file`

File containing long insertions

*_{LI}

`rp`

`meta`
`:map`

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

`*_RP`
`:file`

File containing read-pair evidence

*_{RP}

`si`

`meta`
`:map`

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

`*_SI`
`:file`

File containing short insertions

*_{SI}

`td`

`meta`
`:map`

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

`*_TD`
`:file`

File containing tandem duplications

*_{TD}

`versions_pindel`

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

The name of the process

`pindel`
`:string`

The name of the tool

`pindel | grep '^Pindel version' | uniq | sed 's/Pindel version //; s/, [0-9]\+.//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`pindel`
`:string`

The name of the tool

`pindel | grep '^Pindel version' | uniq | sed 's/Pindel version //; s/, [0-9]\+.//'`
`:eval`

The expression to obtain the version of the tool

Tools

pindel
GPL v3

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data

gmt.genome.wustl.edu/packages/pindel gmt.genome.wustl.edu/packages/pindel/user-manual