A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
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README.md

README.md

SURVIVOR_ant

A framework to annotate SVs (vcf file) with previous known SVs (vcf file) and or with genomic features (gff and or bed files).


INSTALL:

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 .. 

Test data:

Can be found here: https://github.com/NCBI-Hackathons/svcompare


USAGE:

./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.


CONTACT:

If you have questions or encounter a problem please contact: fritz.sedlazeck@gmail.com