DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

DELLY (Version: 0.5.5) Contact: Tobias Rausch (rausch@embl.de)

Generic options:

-? [ --help ] show help message -t [ --type ] arg (=DEL) SV analysis type (DEL, DUP, INV, TRA) -o [ --outfile ] arg (="sv.vcf") SV output file -x [ --exclude ] arg (="") file with chr to exclude

PE options:

-q [ --map-qual ] arg (=0) min. paired-end mapping quality -s [ --mad-cutoff ] arg (=5) insert size cutoff, median+s*MAD (deletions only)

SR options:

-g [ --genome ] arg genome fasta file -m [ --min-flank ] arg (=13) minimum flanking sequence size

Genotyping options:

-v [ --vcfgeno ] arg (="site.vcf") input vcf file for genotyping only -u [ --geno-qual ] arg (=20) min. mapping quality for genotyping