svtools简介

svtools - Comprehensive utilities to explore structural variations in genomes

svtools不仅是一个工具，更因为它带有许多子命令而形成一套工具，旨在帮助生物信息工作者构建和探索群体水平的结构变异召回信息。它能够在成千上万样本水平上高效的对speedseq sv软件结构进行合并和分型分析。

依赖信息

具有bash、awk和sort命令的Linux系统；

cnvnator-multi

python2.7（Numpy、Scipy、Pandas、Statsmodels、SVTyper0.7.0）

安装

推荐使用pip安装，方便快捷

pip install svtools

命令及含义

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