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);