A framework to annotate SVs (vcf file) with previous known SVs (vcf file) and or with genomic features (gff and or bed files).
Download SURVIVOR:
git clone https://github.com/fritzsedlazeck/SURVIVOR_ant.git
cd SURVIVOR_ant
mkdir build
cd build
cmake ..
make
cd ../bin/survivor_ant-core-0.1.0
Note Mac users often have to provide parameters to the cmake command:
cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 ..
Can be found here: https://github.com/NCBI-Hackathons/svcompare
./survivor_ant --help
./survivor_ant [-o ] [-l ] [-v ] [-g ] [-b ] [--anno_distance ] [--svs_distance ] -i [--] [--version] [-h]
Where:
-o , --output output file name
-l , --min_length Minimum length of SV to be reported. Default: 20
-v , --vcf VCF input file name(s)
-g , --gff gff annotation(s)
-b , --bed bed annotation(s)
--anno_distance Maximum distance to assign annotations to SVs. Default: 1000
--svs_distance Maximum distance to group SV together. Default: 1000
-i , --svvcf (required) The vcf file that we should annotate
--, --ignore_rest Ignores the rest of the labeled arguments following this flag.
--version Displays version information and exits.
-h, --help Displays usage information and exits.
If you have questions or encounter a problem please contact: fritz.sedlazeck@gmail.com