svtools - Comprehensive utilities to explore structural variations in genomes
svtools is a suite of utilities designed to help bioinformaticians construct and explore cohort-level structural variation calls. It is designed to efficiently merge and genotype calls from
speedseq sv across thousands to tens of thousands of genomes.
Table of Contents
- A Linux-like environment with bash, awk, and sort
- A working installation of
cnvnator-multi(a component of
We recommend you install using
conda, but you may also install via
pip. For more detailed instructions, see our Installation guide.
Installing via conda
conda install -c bioconda svtools
Installing via pip
pip install svtools
Please see the documentation on, or linked to, this page. For additional help or to report a bug, please open an issue in the
svtools repository: https://github.com/hall-lab/svtools/issues
svtools consists of subcommands for processing VCF or BEDPE files of structural variants and one accessory script (
usage: svtools [-h] [--version] [--support] subcommand ... Comprehensive utilities to explore structural variation in genomes optional arguments: -h, --help show this help message and exit --version show program's version number and exit --support information on obtaining support subcommand description lsort sort N LUMPY VCF files into a single file lmerge merge LUMPY calls inside a single file from svtools lsort vcfpaste paste VCFs from multiple samples copynumber add copynumber information using cnvnator-multi genotype compute genotype of structural variants based on breakpoint depth afreq add allele frequency information to a VCF file bedpetobed12 convert a BEDPE file to BED12 format for viewing in IGV or the UCSC browser bedpetovcf convert a BEDPE file to VCF vcftobedpe convert a VCF file to a BEDPE file vcfsort sort a VCF file bedpesort sort a BEDPE file prune cluster and prune a BEDPE file by position based on allele frequency varlookup look for variants common between two BEDPE files classify reclassify DEL and DUP based on read depth information
svtools is published, please cite using its DOI. Note that this link corresponds to the latest version. If you used an earlier version then your DOI may be different and you can find it on Zenodo.
As issues arise and common problems are identified, we will list them here.
Note: For additional information and usage refer to the Tutorial.md file.