RMA Hunter

This project was moved here → https://github.com/bioinf/RMAhunter

http://rmahunter.bioinf.me/
http://rma-hunter.cf:8915

This is RMA Hunter — a web-based tool to systematically analyze and correct reference minor alleles in variant calling data. The tool provides a complete list of all potentially interesting RMAs that are not called in the sample analyzed or found reference homo-/heterozygous, as well as all reference-synonymous variants called in the RMA loci. All variants are annotated with correct pathogenicity predictions and reference allele frequencies.

To start, please upload your VCF file and (for exome sequencing or target sequencing assays) a BED-file containing enrichment intervals. To analyze only specific genes of interest, please enter a list of genes (separate with comma or a newline) in the box provided.

Please cite the tool as:
Barbitoff Y.A., Bezdvornykh I.V., Serebryakova E.A., Glotov A.S., Glotov O.S. and Predeus A.V.
Systematic correction of reference minor alleles in clinical variant calling. (2016)

Quick Start

How to install & run local version

git clone https://github.com/bioinf/RMAhunter.git && cd RMAhunter
gzip -d data/RMA_Annotations_NoESP.csv.gz data/RMA_Neighbor_Variants_WithEffs.csv.gz
chmod +x exec/*

Usage:
  ./exec/hunter.py [input vcf-file] [Optional arguments]

Optional arguments:
  -f  Path to `input.vcf` file
  -v  Show log [N or Y]. Default: Y
  -c  Report coding only [N or Y]. Default: Y
  -g  Analyze specific gene set [Comma separated list of genes]
  -m  Allelic frequency cutoff. Default: 0.01
  -o  Output dir name
  -z  Show non-calls [N or Y]. Default: Y

Examples:
  ./exec/hunter.py input.vcf
  ./exec/hunter.py -f input.vcf -c 0 -m 0.05 -o results
  ./exec/hunter.py -f input.vcf -g TLX1NB,USP17L25,TCP11X2,SFRP1,CAP1

How to start a server with a web-version

Install Node.JS, npm, forever. Example (ubuntu):

curl -sL https://deb.nodesource.com/setup_6.x | sudo -E bash -
sudo apt install -y nodejs npm
npm install forever -g
npm install

Compress HTML, JS and CSS files

./exec/build.py

Make demo samples

gzip -d data/example.vcf.gz
cp data/example.vcf /tmp/demo.xvcf && touch /tmp/demo.xbed
./exec/app.sh demo Y N 0.01

Starting web-server on port 8915

nodejs ./exec/hunter.js 8915 # for debug
forever start ./exec/hunter.js 8915 # for production

If file data/RMA_Annotations_NoESP.csv has been updated, you need to create a file with a list of genes for the web version:

echo "exports.e = {" $(
  echo $(
   cat data/RMA_Annotations_NoESP.csv | \
    awk -F  "," {'print $6'} | sort | uniq | \
    awk '{print "\""$1"\":true"}'
  ) | sed 's/ /,/g'
) "}" > exec/genes.js