This project was moved here → https://github.com/bioinf/RMAhunter
http:https://rmahunter.bioinf.me/
http:https://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)
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
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