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’]

bam:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bam_index:file

Index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

vcf:file

Matching VCF of alignments

*.vcf

meta2:map

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

fasta:file

FASTA file used to generate alignments

*.{fa,fasta}

meta2:map

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

fai:file

FAI file used to generate alignments

*.{fai}

Output

name:type
description
pattern

json

meta:map

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

*.json:file

JSON file including Library information

*.json

gt_vcf

meta:map

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

*.vcf:file

Genotyped SVs

*.vcf

bam

meta:map

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

*.bam:file

BAM file with

*.bam

versions

versions.yml:file

File containing software versions

versions.yml

Tools

svtyper
MIT

Compute genotype of structural variants based on breakpoint depth

github.com/hall-lab/svtyper 10.1038/nmeth.3505
Github user kubranarci
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