svtools - Comprehensive utilities to explore structural variations in genomes
Summary
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
Requirements
- A Linux-like environment with bash, awk, and sort
- A working installation of
cnvnator-multi(a component ofspeedseq sv) - Python2.7
- Numpy
- Scipy
- Pandas
- Statsmodels
- SVTyper (0.7.0)
Installation
We recommend you install using pip. For more detailed instructions, see our Installation guide.
Installing via pip
pip install svtools
Obtaining help
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
Usage
svtools consists of subcommands for processing VCF or BEDPE files of structural variants and one accessory script (create_coordinates).
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
Citing svtools
Until 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.
Troubleshooting
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.