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
-
clone repo
git clone https://github.com/vanNul/sver
-
compile
cd sver
./autogen.sh
./configure --prefix=/path/to/install/dir/
make
make install
-
execute
/path/to/install/dir/sver