A toolkit to detect and flag potentially false SV's based on SNP's and coverage. Hackathon team: Lead: Fritz Sedlazeck - SysAdmin: Steve Osazuwa - Programmers: Priya Krithivasan, Kshithija Nagulapalli, David Oliver, Seungyeul Yoo
Input requirements
- bam file
- Structural Variants in vcf format
- Gold Standard SV callset
git clone -r https://github.com/NCBI-Hackathons/ScrubSV.git
cd ScrubSV
Refer to https://github.com/vibansal/HapCUT2 for installation instructions
Refer to https://github.com/fritzsedlazeck/SURVIVOR for installation instructions. Move the executable to the current working directory.
vcftools and Genomic Ranges
Install vcftools
sudo apt-get vcftools
Install GenomicRanges
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
library(GenomicRanges)
We created and presented this method over the NYGC NCBI Hackathon in August 2018. Here is the link to the slides
We included a workflow of our pipeline describing the modules in the repo. Feel free to check it out.