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

bed (file)

BED file containing regions of interest

fasta (file)

Input reference genome fasta file

fai (file)

Input reference genome fasta index file

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bp (file)

File containing breakpoints

*_{BP}

cem (file)

File containing close end reads

*_{CloseEndMapped}

del (file)

File containing deletions

*_{D}

dd (file)

File containing dispersed duplications

*_{DD}

int_{final (file)

File containing interchromosomal events

*_{INT_final}

inv (file)

File containing inversions

*_{INV}

li (file)

File containing long insertions

*_{LI}

rp (file)

File containing read-pair evidence

*_{RP}

si (file)

File containing short insertions

*_{SI}

td (file)

File containing tandem duplications

*_{TD}
author
Github user marrip
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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