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# Variant annotation before the running GAVIN-Plus interpretation tool
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# Suppose your file is called 'myexome.vcf', set filename variable to:
FILENAME=myexome

# ** FOR ANY ENVIRONMENT **
# Download core annotation tools and data sources
wget https://github.com/molgenis/molgenis/releases/download/v1.21.1/CmdLineAnnotator-1.21.1.jar
wget https://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip
wget http://krishna.gs.washington.edu/download/CADD/v1.3/whole_genome_SNVs.tsv.gz
wget http://krishna.gs.washington.edu/download/CADD/v1.3/whole_genome_SNVs.tsv.gz.tbi
wget ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz
wget ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz.tbi
# Run annotations for SnpEff, ExAC, and CADD
java -Xmx4g -jar snpEff/snpEff.jar hg19 -noStats -noLog -lof -canon -ud 0 $FILENAME.vcf > $FILENAME.snpeff.vcf
java -Xmx4g -jar CmdLineAnnotator-1.21.1.jar -a exac -s ExAC.r0.3.sites.vep.vcf.gz -i $FILENAME.snpeff.vcf -o $FILENAME.snpeff.exac.vcf
java -Xmx4g -jar CmdLineAnnotator-1.21.1.jar -a cadd -s whole_genome_SNVs.tsv.gz -i $FILENAME.snpeff.exac.vcf -o $FILENAME.snpeff.exac.caddsnv.vcf

# ** FOR UMCG/RUG CLUSTER ENVIRONMENT **
# Load dependencies
module load snpEff/4.3-Java-1.7.0_80
module load CmdLineAnnotator/1.21.1-Java-1.8.0_45
# Run annotations for SnpEff, ExAC, GoNL, CADD and 1000G
java -Xmx4g -jar ${EBROOTSNPEFF}/snpEff.jar hg19 -noStats -noLog -lof -canon -ud 0 $FILENAME.vcf > $FILENAME.snpeff.vcf
java -Xmx4g -jar ${EBROOTCMDLINEANNOTATOR}/CmdLineAnnotator-1.21.1.jar -a exac -s /groups/umcg-pub/prm02/resources/exac/ExAC.r0.3.sites.vep.vcf.gz -i $FILENAME.snpeff.vcf -o $FILENAME.snpeff.exac.vcf
java -Xmx4g -jar ${EBROOTCMDLINEANNOTATOR}/CmdLineAnnotator-1.21.1.jar -a gonl -s /groups/umcg-pub/prm02/resources/gonl/release5_noContam_noChildren_with_AN_AC_GTC_stripped/ -i $FILENAME.snpeff.exac.vcf -o $FILENAME.snpeff.exac.gonl.vcf
java -Xmx4g -jar ${EBROOTCMDLINEANNOTATOR}/CmdLineAnnotator-1.21.1.jar -a cadd -s /groups/umcg-pub/prm02/resources/cadd/whole_genome_SNVs.tsv.gz -i $FILENAME.snpeff.exac.gonl.vcf -o $FILENAME.snpeff.exac.gonl.caddsnv.vcf
java -Xmx4g -jar ${EBROOTCMDLINEANNOTATOR}/CmdLineAnnotator-1.21.1.jar -a thousandGenomes -s /groups/umcg-pub/prm02/resources/1000G/ -i $FILENAME.snpeff.exac.gonl.caddsnv.vcf -o $FILENAME.snpeff.exac.gonl.caddsnv.1kg.vcf