NibblerSV

Fading out to https://github.com/brentp/nibsv <--

Intro

nibsv genotypes base-resolved structural variants by counting the occurence of novel k-mers generated at the break-points.

This means that nibsv has very high specificity, but because there are some SVs that do not generate novel k-mers, it can have a lower sensitivity.

Usage

To run nibsv, download the static binary from the releases and run as:

nibsv -o ${genotyped_vcf} \
  -k 13 --space 17 --space 18 \
  ${sites_vcf}  ${bam_or_cram} ${reference_fasta}

Full usage:

[nibsv] version: 0.0.2 commit: b1b9e06937d519fed27f9032b26a285367106354
nibsv

Usage:
  nibsv [options] vcf bam ref

Arguments:
  vcf              SV vcf with sites to genotype
  bam              bam or cram file for sample
  ref              reference fasta file

Options:
  -k=K                       kmer-size must be <= 15 if space > 0 else 31 (default: 27)
  --space=SPACE              space between kmers (can be specified multiple times)
  -o=O                       output vcf (default: nibsv.vcf.gz)
  --cram-ref=CRAM_REF        optional reference fasta file for cram if difference from reference fasta
  -h, --help                 Show this help

Contributors

Brent Pedersen¹, Christopher Dunn², Eric Dawson³, Fritz Sedlazeck⁴, Peter Xie⁵, and Zev Kronenberg²

¹ University of Utrecht; ²PacBio; ³Nvidia Corporation; ⁴Baylor College of Medicine; ⁵JBrowse (UC Berkeley);