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{:bash}

: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{:bash}

:file

BAM file

*.bam

bai{:bash}

:file

BAM index file

*.bai

fasta{:bash}

:file

Input reference genome fasta file

fai{:bash}

:file

Input reference genome fasta index file

bed{:bash}

:file

BED file containing regions of interest

Output

name:type
description
pattern

bp{:bash}

meta{:bash}

:map

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

*_BP{:bash}

:file

File containing breakpoints

*_{BP}

cem{:bash}

meta{:bash}

:map

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

*_CloseEndMapped{:bash}

:file

File containing close end reads

*_{CloseEndMapped}

del{:bash}

meta{:bash}

:map

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

*_D{:bash}

:file

File containing deletions

*_{D}

dd{:bash}

meta{:bash}

:map

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

*_DD{:bash}

:file

File containing dispersed duplications

*_{DD}

int_final{:bash}

meta{:bash}

:map

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

*_INT_final{:bash}

:file

int file

*_INT_final

inv{:bash}

meta{:bash}

:map

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

*_INV{:bash}

:file

File containing inversions

*_{INV}

li{:bash}

meta{:bash}

:map

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

*_LI{:bash}

:file

File containing long insertions

*_{LI}

rp{:bash}

meta{:bash}

:map

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

*_RP{:bash}

:file

File containing read-pair evidence

*_{RP}

si{:bash}

meta{:bash}

:map

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

*_SI{:bash}

:file

File containing short insertions

*_{SI}

td{:bash}

meta{:bash}

:map

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

*_TD{:bash}

:file

File containing tandem duplications

*_{TD}

versions{:bash}

versions.yml{:bash}

: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
maintainer
Github user marrip
get in touch
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