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

1. Requirements
2. Installation
3. Obtaining help
4. Usage
5. Citing svtools
6. Troubleshooting

Requirements

• A Linux-like environment with bash, awk, and sort
• A working installation of cnvnator-multi (a component of speedseq sv)
• Python2.7
  • Numpy
  • Scipy
  • Pandas
  • Statsmodels
  • Pysam (≥0.8.1)

Installation

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

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.