vep.sh

nohup vep --compress_output bgzip --fork 40 --dir /opt/vep/.vep --af --appris --biotype --buffer_size 8000 --force_overwrite --flag_pick --check_existing --canonical --distance 5000 --mane --polyphen b --pubmed --regulatory --sift b --species homo_sapiens --symbol --transcript_version --tsl --cache --input_file input.vcf.gz --output_file output.vcf.gz --vcf --plugin Phenotypes --plugin miRNA --fasta ./GRCh38p5/Homo_sapiens.GRCh38.dna.primary_assembly.fa --plugin DisGeNET,file=/root/VEP/VEP_100/resources/DisGeNET/all_variant_disease_pmid_associations_final.tsv.gz,disease=1,rsid=1 --plugin GeneSplicer,/root/GeneSplicer/GeneSplicer/sources/genesplicer,/root/GeneSplicer/GeneSplicer/human,tmpdir=/root/VEP/tmp --plugin dbNSFP,/root/VEP/VEP_100/resources/dbNSFP4.0a/dbNSFP4.0a.gz,rs_dbSNP151,SIFT_score,SIFT_converted_rankscore,SIFT_pred,SIFT4G_score,SIFT4G_converted_rankscore,SIFT4G_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,CADD_raw,CADD_raw_rankscore,CADD_phred,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,1000Gp3_AC,1000Gp3_AF,1000Gp3_AFR_AC,1000Gp3_AFR_AF,1000Gp3_EUR_AC,1000Gp3_EUR_AF,1000Gp3_AMR_AC,1000Gp3_AMR_AF,1000Gp3_EAS_AC,1000Gp3_EAS_AF,1000Gp3_SAS_AC,1000Gp3_SAS_AF,ESP6500_AA_AC,ESP6500_AA_AF,ESP6500_EA_AC,ESP6500_EA_AF,ExAC_AC,ExAC_AF,ExAC_Adj_AC,ExAC_Adj_AF,ExAC_AFR_AC,ExAC_AFR_AF,ExAC_AMR_AC,ExAC_AMR_AF,ExAC_EAS_AC,ExAC_EAS_AF,ExAC_FIN_AC,ExAC_FIN_AF,ExAC_NFE_AC,ExAC_NFE_AF,ExAC_SAS_AC,ExAC_SAS_AF,gnomAD_exomes_AC,gnomAD_exomes_AN,gnomAD_exomes_AF,gnomAD_exomes_nhomalt,gnomAD_exomes_AFR_AC,gnomAD_exomes_AFR_AN,gnomAD_exomes_AFR_AF,gnomAD_exomes_AFR_nhomalt,gnomAD_exomes_AMR_AC,gnomAD_exomes_AMR_AN,gnomAD_exomes_AMR_AF,gnomAD_exomes_AMR_nhomalt,gnomAD_exomes_ASJ_AC,gnomAD_exomes_ASJ_AN,gnomAD_exomes_ASJ_AF,gnomAD_exomes_ASJ_nhomalt,gnomAD_exomes_EAS_AC,gnomAD_exomes_EAS_AN,gnomAD_exomes_EAS_AF,gnomAD_exomes_EAS_nhomalt,gnomAD_exomes_FIN_AC,gnomAD_exomes_FIN_AN,gnomAD_exomes_FIN_AF,gnomAD_exomes_FIN_nhomalt,gnomAD_exomes_NFE_AC,gnomAD_exomes_NFE_AN,gnomAD_exomes_NFE_AF,gnomAD_exomes_NFE_nhomalt,gnomAD_exomes_SAS_AC,gnomAD_exomes_SAS_AN,gnomAD_exomes_SAS_AF,gnomAD_exomes_SAS_nhomalt,gnomAD_exomes_POPMAX_AC,gnomAD_exomes_POPMAX_AN,gnomAD_exomes_POPMAX_AF,gnomAD_exomes_POPMAX_nhomalt,gnomAD_genomes_AC,gnomAD_genomes_AN,gnomAD_genomes_AF,gnomAD_genomes_nhomalt,gnomAD_genomes_AFR_AC,gnomAD_genomes_AFR_AN,gnomAD_genomes_AFR_AF,gnomAD_genomes_AFR_nhomalt,gnomAD_genomes_AMR_AC,gnomAD_genomes_AMR_AN,gnomAD_genomes_AMR_AF,gnomAD_genomes_AMR_nhomalt,gnomAD_genomes_ASJ_AC,gnomAD_genomes_ASJ_AN,gnomAD_genomes_ASJ_AF,gnomAD_genomes_ASJ_nhomalt,gnomAD_genomes_EAS_AC,gnomAD_genomes_EAS_AN,gnomAD_genomes_EAS_AF,gnomAD_genomes_EAS_nhomalt,gnomAD_genomes_FIN_AC,gnomAD_genomes_FIN_AN,gnomAD_genomes_FIN_AF,gnomAD_genomes_FIN_nhomalt,gnomAD_genomes_NFE_AC,gnomAD_genomes_NFE_AN,gnomAD_genomes_NFE_AF,gnomAD_genomes_NFE_nhomalt,gnomAD_genomes_POPMAX_AC,gnomAD_genomes_POPMAX_AN,gnomAD_genomes_POPMAX_AF,gnomAD_genomes_POPMAX_nhomalt,clinvar_id,clinvar_clnsig,clinvar_trait,clinvar_review,clinvar_hgvs,clinvar_var_source,clinvar_MedGen_id,clinvar_OMIM_id,clinvar_Orphanet_id,Interpro_domain,Ancestral_allele --plugin LoF,loftee_path:/root/loftee --custom /root/VEP/VEP_100/resources/ClinVar/clinvar.vcf.gz,ClinVar,vcf,exact,0,ALLELEID,CLNDN,CLNDNINCL,CLNDISDB,CLNDISDBINCL,CLNHGVS,CLNREVSTAT,CLNSIG,CLNSIGCONF,CLNSIGINCL,CLNVC,CLNVCSO,CLNVI,DBVARID,GENEINFO,MC,ORIGIN,RS,SSR --custom /root/VEP/VEP_100/resources/CIViC/nightly-civic_accepted_lifted_over.vcf.gz,CIVIC,vcf,exact,0,CSQ,GN,ReverseComplementedAlleles,SwappedAlleles,VT --custom /root/VEP/VEP_100/resources/gnomADr2.1.1/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz,gnomADexome.r2.1.1,vcf,exact,0,AF,AF_afr,AF_amr,AF_asj,AF_eas,AF_fin,AF_nfe,AF_oth,AF_sas,AC,AC_eas,AN,AN_eas >nohup.out_VEP 2>&1 &