## Download GAVIN-APP and data bundle
mkdir gavin-tools
cd gavin-tools
wget http://molgenis.org/downloads/gavin/GAVIN-APP-0.0.1-testing.jar
wget http://molgenis.org/downloads/gavin/required_data_bundle_r0.1/CGD_1jun2016.txt.gz
wget http://molgenis.org/downloads/gavin/required_data_bundle_r0.1/FDR_allGenes.tsv
wget http://molgenis.org/downloads/gavin/required_data_bundle_r0.1/GAVIN_calibrations_r0.1.tsv
wget http://molgenis.org/downloads/gavin/required_data_bundle_r0.1/clinvar.patho.fix.5.5.16.vcf.gz
cd ..

## Download demo files (note that the VCF has been
## annotated by SnpEff, ExAC, GoNL and CADD-SNVs)
wget http://molgenis.org/downloads/gavin/demo/GAVIN-APP_Demo_1000G_Spiked.vcf
wget http://molgenis.org/downloads/gavin/demo/GAVIN-APP_Demo_1000G_Spiked.fromCadd.tsv

## Run analysis on GAVIN-APP_Demo_1000G_Spiked.vcf
java -Xmx4g -jar gavin-tools/GAVIN-APP-0.0.1-testing.jar -i GAVIN-APP_Demo_1000G_Spiked.vcf -o GAVIN-APP_Demo_1000G_Spiked.RVCF.firstpass.vcf -m CREATEFILEFORCADD -a GAVIN-APP_Demo_1000G_Spiked.toCadd.tsv -c gavin-tools/clinvar.patho.fix.5.5.16.vcf.gz -d gavin-tools/CGD_1jun2016.txt.gz -f gavin-tools/FDR_allGenes.tsv -g gavin-tools/GAVIN_calibrations_r0.1.tsv

## Inspect the results, how many interesting variants did we find?
grep -v "#" GAVIN-APP_Demo_1000G_Spiked.RVCF.firstpass.vcf | wc -l

## Note that not all variants could be assessed due to missing CADD scores
## these are written out in this file, which can be uploaded and scores
## using the CADD web service (http://cadd.gs.washington.edu/score)
more GAVIN-APP_Demo_1000G_Spiked.toCadd.tsv

## However - the output is included in the demo files for your convenience.
## Use GAVIN-APP_Demo_1000G_Spiked.fromCadd.tsv to run the complete analysis:
java -Xmx4g -jar gavin-tools/GAVIN-APP-0.0.1-testing.jar -i GAVIN-APP_Demo_1000G_Spiked.vcf -o GAVIN-APP_Demo_1000G_Spiked.RVCF.vcf -m ANALYSIS -a GAVIN-APP_Demo_1000G_Spiked.fromCadd.tsv -c gavin-tools/clinvar.patho.fix.5.5.16.vcf.gz -d gavin-tools/CGD_1jun2016.txt.gz -f gavin-tools/FDR_allGenes.tsv -g gavin-tools/GAVIN_calibrations_r0.1.tsv

## Inspect the results, how many variants are there now?
grep -v "#" GAVIN-APP_Demo_1000G_Spiked.RVCF.vcf | wc -l
diff GAVIN-APP_Demo_1000G_Spiked.RVCF.firstpass.vcf GAVIN-APP_Demo_1000G_Spiked.RVCF.vcf