/sver

DNA Structural Variants Finder for NGS

Primary LanguageC++

program: sver
version: 0.0.0
updated: 22:01:59 Aug 6 2019
Usage: sver [OPTIONS]

Options Explanations
-h,--help Print this help message and exit
General:
-b,--bam FILE REQUIRED bam file
-g,--genome FILE REQUIRED reference genome
-a,--anno FILE REQUIRED annotation database file
-r,--reg FILE valid region to disvover SV
-o,--bcfout TEXT=out.bcf output bcf file
-t,--tsvout TEXT=out.tsv output tsv file
-s,--svtype INT in [0 - 4] SV types to discover,0:INV,1:DEL,2:DUP,3:INS,4:BND
-n,--nthread INT in [1 - 20]=8 number of threads used to process bam

Installation

  1. clone repo
    git clone https://github.com/vanNul/sver

  2. compile
    cd sver
    ./autogen.sh
    ./configure --prefix=/path/to/install/dir/
    make make install

  3. execute
    /path/to/install/dir/sver