Description

SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample

Input

name:type
description
pattern

meta:map

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

bam:file

BAM or CRAM file with alignments

*.{bam,cram}

bam_index:file

BAI file matching the BAM file

*.{bai}

vcf:file

Matching VCF of alignments

*.vcf

meta2:map

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

fasta:file

indexed reference FASTA file (recommended for reading CRAM files)

*.{fa,fasta}

Output

name:type
description
pattern

gt_vcf

meta:map

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

*.vcf:file

Genotyped SVs

*.vcf

json

meta:map

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

*.json:file

JSON file including library information

*.json

versions

versions.yml:file

File containing software versions

versions.yml

Tools

svtyper
MIT

Bayesian genotyper for structural variants

github.com/hall-lab/svtyper 10.1038/nmeth.3505
maintainer
Github user tstoeriko
get in touch
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