Description

SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data

Input

Name (Type)
Description
Pattern

meta (map)

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

meta2 (map)

Groovy Map containing sample information for FASTA file
e.g. [ id:‘fasta’]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

vcf (file)

Matching VCF of alignments

*.vcf

fasta (file)

FASTA file used to generate alignments

*.{fa,fasta}

fai (file)

FAI file used to generate alignments

*.{fai}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

json (file)

JSON file including Library information

*.json

gt_vcf (file)

Genotyped SVs

*.vcf

relevant_bam (file)

Relevant alignments

*.bam
author
Github user kubranarci
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Tools

svtyper
MIT

Compute genotype of structural variants based on breakpoint depth

github.com/hall-lab/svtyper 10.1038/nmeth.3505