https://github.com/DCGenomics/NCBI_August_Hackathon_Push_Button_Genomics_Solution/wiki
Commands into SNP Eff to initialize databases for subsequent annotations were:
Though in principle we should probably add ALL databases provided at http://snpeff.sourceforge.net/ the following commands were used to annotate and download databases used by SnpEff:
To select GRCh38.p2 as the ref:
java -Xmx4G -jar snpEff.jar -c ./snpEff.config -v -lof GRCh38.p2.RefSeq.genome examples/test.GRCh38.vcf Note: for this step, it may be necessary to add lines like the following to your snpEff.config if doing this on your local machine: Human genome GRCh38 using RefSeq transcripts GRCh38.p2_genomic.genome : Homo_Sapiens GRCh38 release from NCBI's RefSeq GRCh38.p2.RefSeq.genome : Human genome GRCh38 using RefSeq transcripts
add dbsnp stuff:
java -jar SnpSift.jar annotate -dbsnp test.GRCh38.vcf > test.GRCh38.dbsnp.chr22.vcf add clinvar annotations java -jar SnpSift.jar annotate -clinvar test.GRCh38.dbsnp.vcf > test.GRCh38.dbsnp.clinvar.vcf add carlos's gff:
java -Xmx4G -jar snpEff.jar -c ./snpEff.config -v -interval ./data/GGRCh38.p4_gene.gff test.GRCh38.dbsnp.clinvar.vcf > test.GRCh38.dbsnp.clinvar.gene.vcf add geneId:
java -jar r test.GRCh38.dbsnp.vcf > test.GRCh38.dbsnp.clinvar.vcf