brentp / nibsv

SV genotyping with kmers (created during Baylor hackathon)

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NibblerSV

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, Sairam Behera4, Fritz Sedlazeck4, Peter Xie5, and Zev Kronenberg2

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

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SV genotyping with kmers (created during Baylor hackathon)

License:MIT License


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