SVCompare

Comparison and estimation of breakpoints for SVs across different technologies and resources. Summaries of SV annotations.

Introduction:

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

Installation

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

Repo content

test_data:

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.

Citation: