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`

`versions.yml:file`

File containing software versions

versions.yml

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