Comparison and estimation of breakpoints for SVs across different technologies and resources. Summaries of SV annotations.
This github represents a collection of the methods that our group developed to analyze, annotate and more accurately predict breakpoints for SVs on the hackathon (08/15-08/17 @ NIH).
The methods developed consists of:
- SURVIVOR_ant: a comparison and annotate method for a given vcf file.
- generate_statistics.pl: provides statics of callsets in which an event is supported.
- run_all: wrapper for generate_statistics.pl
svcompare tool can be in installed at the root system level or at the user local.
- clone the repository
- gunzip svcompare.zip
- place svcompare folder in a desired location
- GIAB_H002_081716.vcf.zip: includes the merged calls of GIAB HG002 based on 16 call sets.
- GIAB_H002_081716.vcf_anno.zip: The resulting file from SURVIVOR_ant based on the merged file of GIAB HG002.
- caller_tech.map.txt: table linking callers and technologies to use in statistics generation.
please cite our article if you use parts of our methods or data sets. (will soon be announced)