RMA Hunter

http://rmahunter.bioinf.me/

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.

Reference

Barbitoff YA, Bezdvornykh IV, Polev DE, Serebryakova EA, Glotov AS, Glotov OS, Predeus AV, Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling, Genetics in Medicine 2018, 20(3), 360–364.

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

Instead of forever, you can use nodemon

sudo npm install -g nodemon

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 (using forever)
nohup nodemon ./exec/hunter.js 8915 </dev/null &   # for production (using nodemon)

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

Contacts

If you have any questions, please contact Yury A Barbitoff (barbitoff at bioinf me) or Alexander V Predeus (predeus at bioinf me).