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annotator.sh
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#!/usr/bin/env bash
#$ -P prod
#$ -N CHIP_ANNOTATOR
#$ -A 220131_PESA_HLA
#$ -l thread=4
#$ -l h_vmem=32G
#$ -o ejemplo_annotator.stdout
#$ -e ejemplo_annotator.stderr
#Juan Ignacio Alvarez Arenas
source /programs/conda_genomics/envs/vep.sh
cd /data3/220919_CHIP_Annotator/_data
vep --offline --cache --refseq -species homo_sapiens --cache_version 105 --dir_cache /data3/genomes/homo_sapiens/annotations/VEP --dir_plugins /data3/genomes/homo_sapiens/annotations/VEP/Plugins/release_105 --use_transcript_ref --fasta /data3/genomes/homo_sapiens/GATK_bundle/BROAD_hg38/v0/GRCh38.primary_assembly.genome.fa -i ejemplo.vcf.gz -o ejemplo_annotated.vcf.gz --vcf --compress_output gzip -gene_phenotype Cancer Gene Census ClinVar COSMIC HGMD-PUBLIC NHGRI-EBI GWAS catalog --check_existing --everything --humdiv --no_stats --plugin CADD,"/data3/genomes/homo_sapiens/annotations/CADD/v1.6/GRCh38/whole_genome_SNVs.tsv.gz" --plugin LoFtool,"/data3/genomes/homo_sapiens/annotations/VEP/Plugins/release_105/LoFtool_scores.txt" --plugin Mastermind,"/data3/genomes/homo_sapiens/annotations/Mastermind/mastermind_cited_variants_reference-2019.09.27-grch38.vcf.gz" --plugin satMutMPRA,file="/data3/genomes/homo_sapiens/annotations/satMutMPRA/satMutMPRA_GRCh38_ALL.tsv.gz" --plugin dbNSFP,"/data3/genomes/Homo_sapiens/annotations/dbNSFP/dbNSFP/dbNSFP4.3a_grch38.gz,chr,ref,alt,aaref,aaalt,rs_dbSNP,hg19_chr,hg18_chr,genename,Ensembl_geneid,Ensembl_transcriptid,Ensembl_proteinid,Uniprot_acc,Uniprot_entry,HGVSc_ANNOVAR,HGVSp_ANNOVAR,HGVSc_snpEff,HGVSp_snpEff,HGVSc_VEP,HGVSp_VEP,APPRIS,GENCODE_basic,TSL,VEP_canonical,cds_strand,refcodon,codonpos,codon_degeneracy,Ancestral_allele,AltaiNeandertal,Denisova,VindijiaNeandertal,ChagyrskayaNeandertal,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,LRT_score,LRT_converted_rankscore,LRT_pred,LRT_Omega,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationTaster_model,MutationTaster_AAE,MutationAssessor_score,MutationAssessor_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_converted_rankscore,FATHMM_pred,PROVEAN_score,PROVEAN_converted_rankscore,PROVEAN_pred,VEST4_score,VEST4_rankscore,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,Reliability_index,MetaRNN_score,MetaRNN_rankscore,MetaRNN_pred,M-CAP_score,M-CAP_rankscore,M-CAP_pred,REVEL_score,REVEL_rankscore,MutPred_score,MutPred_rankscore,MutPred_protID,MutPred_AAchange,MutPred_Top5features,MVP_score,MVP_rankscore,MPC_score,MPC_rankscore,PrimateAI_score,PrimateAI_rankscore,PrimateAI_pred,DEOGEN2_score,DEOGEN2_rankscore,DEOGEN2_pred,BayesDel_addAF_score,BayesDel_addAF_rankscore,BayesDel_addAF_pred,BayesDel_noAF_score,BayesDel_noAF_rankscore,BayesDel_noAF_pred,ClinPred_score,ClinPred_rankscore,ClinPred_pred,LIST-S2_score,LIST-S2_rankscore,LIST-S2_pred,Aloft_Fraction_transcripts_affected,Aloft_prob_Tolerant,Aloft_prob_Recessive,Aloft_prob_Dominant,Aloft_pred,Aloft_Confidence,CADD_raw,CADD_raw_rankscore,CADD_phred,CADD_raw_hg19,CADD_raw_rankscore_hg19,CADD_phred_hg19,DANN_score,DANN_rankscore,fathmm-MKL_coding_score,fathmm-MKL_coding_rankscore,fathmm-MKL_coding_pred,fathmm-MKL_coding_group,fathmm-XF_coding_score,fathmm-XF_coding_rankscore,fathmm-XF_coding_pred,Eigen-raw_coding,Eigen-raw_coding_rankscore,Eigen-phred_coding,Eigen-PC-raw_coding,Eigen-PC-raw_coding_rankscore,Eigen-PC-phred_coding,GenoCanyon_score,GenoCanyon_rankscore,integrated_fitCons_score,integrated_fitCons_rankscore,integrated_confidence_value,GM12878_fitCons_score,GM12878_fitCons_rankscore,GM12878_confidence_value,H1-hESC_fitCons_score,H1-hESC_fitCons_rankscore,H1-hESC_confidence_value,HUVEC_fitCons_score,HUVEC_fitCons_rankscore,HUVEC_confidence_value,LINSIGHT,LINSIGHT_rankscore,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phyloP30way_mammalian,phyloP30way_mammalian_rankscore,phyloP17way_primate,phyloP17way_primate_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,phastCons30way_mammalian,phastCons30way_mammalian_rankscore,phastCons17way_primate,phastCons17way_primate_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,bStatistic,bStatistic_converted_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,TWINSUK_AC,TWINSUK_AF,ALSPAC_AC,ALSPAC_AF,UK10K_AC,UK10K_AF,ESP6500_AA_AC,ESP6500_AA_AF,ESP6500_EA_AC,ESP6500_EA_AF,ExAC_AC,ExAC_AF,gnomAD_exomes_flag,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_flag,gnomAD_genomes_AC,gnomAD_genomes_AN,gnomAD_genomes_AF,gnomAD_genomes_nhomalt,gnomAD_genomes_POPMAX_AC,gnomAD_genomes_POPMAX_AN,gnomAD_genomes_POPMAX_AF,gnomAD_genomes_POPMAX_nhomalt,gnomAD_genomes_AFR_AC,gnomAD_genomes_AFR_AN,gnomAD_genomes_AFR_AF,gnomAD_genomes_AFR_nhomalt,gnomAD_genomes_AMI_AC,gnomAD_genomes_AMI_AN,gnomAD_genomes_AMI_AF,gnomAD_genomes_AMI_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_MID_AC,gnomAD_genomes_MID_AN,gnomAD_genomes_MID_AF,gnomAD_genomes_MID_nhomalt,gnomAD_genomes_NFE_AC,gnomAD_genomes_NFE_AN,gnomAD_genomes_NFE_AF,gnomAD_genomes_NFE_nhomalt,gnomAD_genomes_SAS_AC,gnomAD_genomes_SAS_AN,gnomAD_genomes_SAS_AF,gnomAD_genomes_SAS_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,GTEx_V8_gene,GTEx_V8_tissue,Geuvadis_eQTL_target_gene"