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

, 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

]

*_BP:file

File containing breakpoints

*_{BP}

cem

meta:map

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

]

*_CloseEndMapped:file

File containing close end reads

*_{CloseEndMapped}

del

meta:map

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

]

*_D:file

File containing deletions

*_{D}

dd

meta:map

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

]

*_DD:file

File containing dispersed duplications

*_{DD}

int_final

meta:map

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

]

*_INT_final:file

int file

*_INT_final

inv

meta:map

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

]

*_INV:file

File containing inversions

*_{INV}

li

meta:map

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

]

*_LI:file

File containing long insertions

*_{LI}

rp

meta:map

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

]

*_RP:file

File containing read-pair evidence

*_{RP}

si

meta:map

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

]

*_SI:file

File containing short insertions

*_{SI}

td

meta:map

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

]

*_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