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’]

meta2 (map)

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

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

fasta (file)

indexed reference FASTA file (recommended for reading CRAM files)

*.{fa,fasta}

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
maintainer
Github user tstoeriko
get in touch
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Tools

svtyper
MIT

Bayesian genotyper for structural variants

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