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Variant annotation with VEP conda

10 Apr 2023 - last update

How I use ensembl VEP for annotation

http://www.ensembl.org/info/docs/tools/vep/index.html. Using ensembl VEP is made easier by way of conda https://anaconda.org/bioconda/ensembl-vep. A requirement is to have samtools, bcftools, htslib (all at http://www.htslib.org/) also installed with conda. The conda env will allow VEP to run, but we must also have the plugins/databases installed. View a list of databases that I recommend during annotation. Alternatives:

NIRVANA https://illumina.github.io/NirvanaDocumentation/
ANNOVAR https://annovar.openbioinformatics.org/en/latest/

Install with conda

Here is my installation and directions note which I refer to when running VEP with conda.

$ user@cluster:/work/group/user/project/exome/src/joint$ cat conda_vep.txt
I copied this
<https://gist.github.com/ckandoth/d6de7eff889e8860dd5f3f3dd234c045>
but also used conda:

# ###########
# Set up ----
# ###########

mamba create -n vep
conda activate vep

conda install -y -c conda-forge -c bioconda -c defaults ensembl-vep==106.0 htslib==1.14 bcftools==1.14 samtools==1.14

conda deactivate

# ###############
# Set up end ----
# ###############

conda list
conda env list
conda --info envs

# #############
# Reattach ----
# #############

conda activate vep
vep --help
conda deactivate

# ###############
# Work end ----
# ###############

Running VEP with conda

Here is an example script for annotating a VCF output after the GATK SNV pipeline. The major annotation information comes from default VEP data (“–everything” flag). Several plugins are also used, including dbNSFP which for SNVs (but not indel) adds >100 columns of annotation data. After completion I refer back to conda_vep.txt notes to deactivate conda (although automated within the pipeline).

I run it using:

conda activate vep
sbatch annotation_conda.sh

However, I would have this in a workflow pipeline that might have other parameters which would change the structure. This is the basic requirements:

$ user@cluster:/work/group/user/project/src/joint/annotation_conda.sh

#!/bin/bash
#SBATCH --nodes 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 24
#SBATCH --mem 30G
#SBATCH --time 03:00:00
#SBATCH --job-name=vep
#SBATCH --output=./log/vep/vep_%J.out
#SBATCH --error=./log/vep/vep_%J.err
#SBATCH --comment="cost" # custom for cluster

# CONDA ENV
# activate before submission
# conda activate vep

echo "START AT $(date)"
set -e
source ./variables.txt
module load intel # jed

# Path
INPUT_DIR="${WORK_DIR}/pre_annotation_output"
OUTPUT_DIR="${WORK_DIR}/annotation"

# db
DATABASES="/work/group/databases"
REF="/work/group/user/Reference_Genome/GRCH38_no_alt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz"
GTF="/work/group/user/Reference_Genome/GRCH38_no_alt/gtf_and_gff/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf.gz"
GFF="/work/group/user/Reference_Genome/GRCH38_no_alt/gtf_and_gff/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation_for_vep.gff.gz"
PLUGINS="${DATABASES}/vep_hg38/plugins"
LOFTEE="${DATABASES}/vep_hg38/loftee"
CACHE="${DATABASES}/vep_hg38/cache_hg38_ensembl"
CLINVAR="${DATABASES}/clinvar/hg38/20220730/clinvar_20220730.vcf.gz"
CADD_DIR="${DATABASES}/CADD_v1.6_GRCH38_hg38"
REVEL="${DATABASES}/revel/new_tabbed_revel_grch38.tsv.gz"
GNOMAD="/scratch/user/gnomad/gnomad.exomes.r2.0.1.sites.GRCh38.noVEP.vcf.gz"
G2P_PANNEL="/work/group/user/panels/Primary_immunodeficiency.csv"
dbNSFP="/work/group/user/database/dbNSFP/data/dbNSFP4.2a_grch38.gz"
IntAct="/work/group/user/database/intact"
# GNOMAD="${DATABASES}/gnomAD_GRCh38_sites/gnomad.exomes.r2.0.1.sites.GRCh38.noVEP.vcf.gz"
# GNOMAD="${DATABASES}/gnomAD_GRCh38_sites/gnomad.exomes.r2.1.1.sites.liftover_grch38_PASS.vcf.gz"

# VEP
vep \
--fasta $REF \
--offline \
--use_given_ref \
--everything \
--vcf \
--cache \
--dir_cache $CACHE \
--canonical \
--hgvs \
--symbol \
--mane \
--cache_version 104 \
--dir_plugins ${PLUGINS} \
--plugin SpliceConsensus \
--plugin CADD,${CADD_DIR}/whole_genome_SNVs.tsv.gz,${CADD_DIR}/gnomad.genomes.r3.0.indel.tsv.gz \
--plugin dbNSFP,${dbNSFP},ALL \
--custom ${CLINVAR},ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN \
--plugin IntAct,mutation_file=${IntAct}/mutations.tsv,mapping_file=${IntAct}/mutation_gc_map.txt.gz \
--plugin IntAct,mutation_file=${IntAct}/mutations.tsv,mapping_file=${IntAct}/mutation_gc_map.txt.gz,minimal=1 \
-i ${INPUT_DIR}/bcftools_gatk_norm.vcf.gz \
-o ${OUTPUT_DIR}/bcftools_gatk_norm_vep_conda_plug.vcf \
--fork 24 \
--force_overwrite

# # vep custom annotation
# ./vep [...] --custom Filename , Short_name , File_type , Annotation_type , Force_report_coordinates , VCF_fields
# # For multiple custom files, use:
# ./vep [...] --custom clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN \
#             --custom TOPMED_GRCh38_20180418.vcf.gz,topmed_20180418,vcf,exact,0,TOPMED \
#             --custom UK10K_COHORT.20160215.sites.GRCh38.vcf.gz,uk10k,vcf,exact,0,AF_ALSPAC
## Where the selected ClinVar INFO fields (from the ClinVar VCF file) are:
# - CLNSIG:     Clinical significance for this single variant
# - CLNREVSTAT: ClinVar review status for the Variation ID
# - CLNDN:      ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB
# Of course you can select the INFO fields you want in the ClinVar VCF file.
# --flag_pick \
# --stats_file ${OUTPUT_DIR}/vep_cache_ensembl_flagpick.html \

echo "END AT $(date)"

Resulting output

The new IFNO columns will contain annotation data that is then used for further filtering, ranking, application of ACMG criteria, etc. for clinical reporting and assigning variant classification:

sample Inheritance genotype SYMBOL HGVSp HGVSc SNP ClinVar_CLNSIG ClinVar_CLNDN ClinVar_CLNREVSTAT genotype_call Consequence IMPACT rownames AC AF.x AN BaseQRankSum DB DP END ExcessHet FS InbreedingCoeff MLEAC MLEAF MQ MQRankSum NEGATIVE_TRAIN_SITE PG POSITIVE_TRAIN_SITE QD RAW_MQandDP ReadPosRankSum SOR VQSLOD culprit OLD_MULTIALLELIC OLD_VARIANT seqnames start end width strand Allele Gene Feature_type Feature BIOTYPE EXON INTRON cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation DISTANCE STRAND FLAGS VARIANT_CLASS SYMBOL_SOURCE HGNC_ID CANONICAL MANE_SELECT MANE_PLUS_CLINICAL TSL APPRIS CCDS ENSP SWISSPROT TREMBL UNIPARC UNIPROT_ISOFORM SOURCE GENE_PHENO SIFT PolyPhen DOMAINS miRNA HGVS_OFFSET AF.y AFR_AF AMR_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF MAX_AF MAX_AF_POPS CLIN_SIG SOMATIC PHENO PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE TRANSCRIPTION_FACTORS SPLICE_CONSENSUS CADD_PHRED CADD_RAW X1000Gp3_AC X1000Gp3_AF X1000Gp3_AFR_AC X1000Gp3_AFR_AF X1000Gp3_AMR_AC X1000Gp3_AMR_AF X1000Gp3_EAS_AC X1000Gp3_EAS_AF X1000Gp3_EUR_AC X1000Gp3_EUR_AF X1000Gp3_SAS_AC X1000Gp3_SAS_AF ALSPAC_AC ALSPAC_AF APPRIS.1 Aloft_Confidence Aloft_Fraction_transcripts_affected Aloft_pred Aloft_prob_Dominant Aloft_prob_Recessive Aloft_prob_Tolerant AltaiNeandertal Ancestral_allele BayesDel_addAF_pred BayesDel_addAF_rankscore BayesDel_addAF_score BayesDel_noAF_pred BayesDel_noAF_rankscore BayesDel_noAF_score CADD_phred CADD_phred_hg19 CADD_raw CADD_raw_hg19 CADD_raw_rankscore CADD_raw_rankscore_hg19 ClinPred_pred ClinPred_rankscore ClinPred_score DANN_rankscore DANN_score DEOGEN2_pred DEOGEN2_rankscore DEOGEN2_score Denisova ESP6500_AA_AC ESP6500_AA_AF ESP6500_EA_AC ESP6500_EA_AF Eigen.PC.phred_coding Eigen.PC.raw_coding Eigen.PC.raw_coding_rankscore Eigen.phred_coding Eigen.raw_coding Eigen.raw_coding_rankscore Ensembl_geneid Ensembl_proteinid Ensembl_transcriptid ExAC_AC ExAC_AF ExAC_AFR_AC ExAC_AFR_AF ExAC_AMR_AC ExAC_AMR_AF ExAC_Adj_AC ExAC_Adj_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 ExAC_nonTCGA_AC ExAC_nonTCGA_AF ExAC_nonTCGA_AFR_AC ExAC_nonTCGA_AFR_AF ExAC_nonTCGA_AMR_AC ExAC_nonTCGA_AMR_AF ExAC_nonTCGA_Adj_AC ExAC_nonTCGA_Adj_AF ExAC_nonTCGA_EAS_AC ExAC_nonTCGA_EAS_AF ExAC_nonTCGA_FIN_AC ExAC_nonTCGA_FIN_AF ExAC_nonTCGA_NFE_AC ExAC_nonTCGA_NFE_AF ExAC_nonTCGA_SAS_AC ExAC_nonTCGA_SAS_AF ExAC_nonpsych_AC ExAC_nonpsych_AF ExAC_nonpsych_AFR_AC ExAC_nonpsych_AFR_AF ExAC_nonpsych_AMR_AC ExAC_nonpsych_AMR_AF ExAC_nonpsych_Adj_AC ExAC_nonpsych_Adj_AF ExAC_nonpsych_EAS_AC ExAC_nonpsych_EAS_AF ExAC_nonpsych_FIN_AC ExAC_nonpsych_FIN_AF ExAC_nonpsych_NFE_AC ExAC_nonpsych_NFE_AF ExAC_nonpsych_SAS_AC ExAC_nonpsych_SAS_AF FATHMM_converted_rankscore FATHMM_pred FATHMM_score GENCODE_basic GERP.._NR GERP.._RS GERP.._RS_rankscore GM12878_confidence_value GM12878_fitCons_rankscore GM12878_fitCons_score GTEx_V8_gene GTEx_V8_tissue GenoCanyon_rankscore GenoCanyon_score Geuvadis_eQTL_target_gene H1.hESC_confidence_value H1.hESC_fitCons_rankscore H1.hESC_fitCons_score HGVSc_ANNOVAR HGVSc_VEP HGVSc_snpEff HGVSp_ANNOVAR HGVSp_VEP HGVSp_snpEff HUVEC_confidence_value HUVEC_fitCons_rankscore HUVEC_fitCons_score Interpro_domain LINSIGHT LINSIGHT_rankscore LIST.S2_pred LIST.S2_rankscore LIST.S2_score LRT_Omega LRT_converted_rankscore LRT_pred LRT_score M.CAP_pred M.CAP_rankscore M.CAP_score MPC_rankscore MPC_score MVP_rankscore MVP_score MetaLR_pred MetaLR_rankscore MetaLR_score MetaRNN_pred MetaRNN_rankscore MetaRNN_score MetaSVM_pred MetaSVM_rankscore MetaSVM_score MutPred_AAchange MutPred_Top5features MutPred_protID MutPred_rankscore MutPred_score MutationAssessor_pred MutationAssessor_rankscore MutationAssessor_score MutationTaster_AAE MutationTaster_converted_rankscore MutationTaster_model MutationTaster_pred MutationTaster_score PROVEAN_converted_rankscore PROVEAN_pred PROVEAN_score Polyphen2_HDIV_pred Polyphen2_HDIV_rankscore Polyphen2_HDIV_score Polyphen2_HVAR_pred Polyphen2_HVAR_rankscore Polyphen2_HVAR_score PrimateAI_pred PrimateAI_rankscore PrimateAI_score REVEL_rankscore REVEL_score Reliability_index SIFT4G_converted_rankscore SIFT4G_pred SIFT4G_score SIFT_converted_rankscore SIFT_pred SIFT_score SiPhy_29way_logOdds SiPhy_29way_logOdds_rankscore SiPhy_29way_pi TSL.1 TWINSUK_AC TWINSUK_AF UK10K_AC UK10K_AF Uniprot_acc Uniprot_entry VEP_canonical VEST4_rankscore VEST4_score VindijiaNeandertal aaalt aapos aaref alt bStatistic bStatistic_converted_rankscore cds_strand chr clinvar_MedGen_id clinvar_OMIM_id clinvar_Orphanet_id clinvar_clnsig clinvar_hgvs clinvar_id clinvar_review clinvar_trait clinvar_var_source codon_degeneracy codonpos fathmm.MKL_coding_group fathmm.MKL_coding_pred fathmm.MKL_coding_rankscore fathmm.MKL_coding_score fathmm.XF_coding_pred fathmm.XF_coding_rankscore fathmm.XF_coding_score genename gnomAD_exomes_AC gnomAD_exomes_AF gnomAD_exomes_AFR_AC gnomAD_exomes_AFR_AF gnomAD_exomes_AFR_AN gnomAD_exomes_AFR_nhomalt gnomAD_exomes_AMR_AC gnomAD_exomes_AMR_AF gnomAD_exomes_AMR_AN gnomAD_exomes_AMR_nhomalt gnomAD_exomes_AN gnomAD_exomes_ASJ_AC gnomAD_exomes_ASJ_AF gnomAD_exomes_ASJ_AN gnomAD_exomes_ASJ_nhomalt gnomAD_exomes_EAS_AC gnomAD_exomes_EAS_AF gnomAD_exomes_EAS_AN gnomAD_exomes_EAS_nhomalt gnomAD_exomes_FIN_AC gnomAD_exomes_FIN_AF gnomAD_exomes_FIN_AN gnomAD_exomes_FIN_nhomalt gnomAD_exomes_NFE_AC gnomAD_exomes_NFE_AF gnomAD_exomes_NFE_AN gnomAD_exomes_NFE_nhomalt gnomAD_exomes_POPMAX_AC gnomAD_exomes_POPMAX_AF gnomAD_exomes_POPMAX_AN gnomAD_exomes_POPMAX_nhomalt gnomAD_exomes_SAS_AC gnomAD_exomes_SAS_AF gnomAD_exomes_SAS_AN gnomAD_exomes_SAS_nhomalt gnomAD_exomes_controls_AC gnomAD_exomes_controls_AF gnomAD_exomes_controls_AFR_AC gnomAD_exomes_controls_AFR_AF gnomAD_exomes_controls_AFR_AN gnomAD_exomes_controls_AFR_nhomalt gnomAD_exomes_controls_AMR_AC gnomAD_exomes_controls_AMR_AF gnomAD_exomes_controls_AMR_AN gnomAD_exomes_controls_AMR_nhomalt gnomAD_exomes_controls_AN gnomAD_exomes_controls_ASJ_AC gnomAD_exomes_controls_ASJ_AF gnomAD_exomes_controls_ASJ_AN gnomAD_exomes_controls_ASJ_nhomalt gnomAD_exomes_controls_EAS_AC gnomAD_exomes_controls_EAS_AF gnomAD_exomes_controls_EAS_AN gnomAD_exomes_controls_EAS_nhomalt gnomAD_exomes_controls_FIN_AC gnomAD_exomes_controls_FIN_AF gnomAD_exomes_controls_FIN_AN gnomAD_exomes_controls_FIN_nhomalt gnomAD_exomes_controls_NFE_AC gnomAD_exomes_controls_NFE_AF gnomAD_exomes_controls_NFE_AN gnomAD_exomes_controls_NFE_nhomalt gnomAD_exomes_controls_POPMAX_AC gnomAD_exomes_controls_POPMAX_AF gnomAD_exomes_controls_POPMAX_AN gnomAD_exomes_controls_POPMAX_nhomalt gnomAD_exomes_controls_SAS_AC gnomAD_exomes_controls_SAS_AF gnomAD_exomes_controls_SAS_AN gnomAD_exomes_controls_SAS_nhomalt gnomAD_exomes_controls_nhomalt gnomAD_exomes_flag gnomAD_exomes_nhomalt gnomAD_exomes_non_cancer_AC gnomAD_exomes_non_cancer_AF gnomAD_exomes_non_cancer_AFR_AC gnomAD_exomes_non_cancer_AFR_AF gnomAD_exomes_non_cancer_AFR_AN gnomAD_exomes_non_cancer_AFR_nhomalt gnomAD_exomes_non_cancer_AMR_AC gnomAD_exomes_non_cancer_AMR_AF gnomAD_exomes_non_cancer_AMR_AN gnomAD_exomes_non_cancer_AMR_nhomalt gnomAD_exomes_non_cancer_AN gnomAD_exomes_non_cancer_ASJ_AC gnomAD_exomes_non_cancer_ASJ_AF gnomAD_exomes_non_cancer_ASJ_AN gnomAD_exomes_non_cancer_ASJ_nhomalt gnomAD_exomes_non_cancer_EAS_AC gnomAD_exomes_non_cancer_EAS_AF gnomAD_exomes_non_cancer_EAS_AN gnomAD_exomes_non_cancer_EAS_nhomalt gnomAD_exomes_non_cancer_FIN_AC gnomAD_exomes_non_cancer_FIN_AF gnomAD_exomes_non_cancer_FIN_AN gnomAD_exomes_non_cancer_FIN_nhomalt gnomAD_exomes_non_cancer_NFE_AC gnomAD_exomes_non_cancer_NFE_AF gnomAD_exomes_non_cancer_NFE_AN gnomAD_exomes_non_cancer_NFE_nhomalt gnomAD_exomes_non_cancer_POPMAX_AC gnomAD_exomes_non_cancer_POPMAX_AF gnomAD_exomes_non_cancer_POPMAX_AN gnomAD_exomes_non_cancer_POPMAX_nhomalt gnomAD_exomes_non_cancer_SAS_AC gnomAD_exomes_non_cancer_SAS_AF gnomAD_exomes_non_cancer_SAS_AN gnomAD_exomes_non_cancer_SAS_nhomalt gnomAD_exomes_non_cancer_nhomalt gnomAD_exomes_non_neuro_AC gnomAD_exomes_non_neuro_AF gnomAD_exomes_non_neuro_AFR_AC gnomAD_exomes_non_neuro_AFR_AF gnomAD_exomes_non_neuro_AFR_AN gnomAD_exomes_non_neuro_AFR_nhomalt gnomAD_exomes_non_neuro_AMR_AC gnomAD_exomes_non_neuro_AMR_AF gnomAD_exomes_non_neuro_AMR_AN gnomAD_exomes_non_neuro_AMR_nhomalt gnomAD_exomes_non_neuro_AN gnomAD_exomes_non_neuro_ASJ_AC gnomAD_exomes_non_neuro_ASJ_AF gnomAD_exomes_non_neuro_ASJ_AN gnomAD_exomes_non_neuro_ASJ_nhomalt gnomAD_exomes_non_neuro_EAS_AC gnomAD_exomes_non_neuro_EAS_AF gnomAD_exomes_non_neuro_EAS_AN gnomAD_exomes_non_neuro_EAS_nhomalt gnomAD_exomes_non_neuro_FIN_AC gnomAD_exomes_non_neuro_FIN_AF gnomAD_exomes_non_neuro_FIN_AN gnomAD_exomes_non_neuro_FIN_nhomalt gnomAD_exomes_non_neuro_NFE_AC gnomAD_exomes_non_neuro_NFE_AF gnomAD_exomes_non_neuro_NFE_AN gnomAD_exomes_non_neuro_NFE_nhomalt gnomAD_exomes_non_neuro_POPMAX_AC gnomAD_exomes_non_neuro_POPMAX_AF gnomAD_exomes_non_neuro_POPMAX_AN gnomAD_exomes_non_neuro_POPMAX_nhomalt gnomAD_exomes_non_neuro_SAS_AC gnomAD_exomes_non_neuro_SAS_AF gnomAD_exomes_non_neuro_SAS_AN gnomAD_exomes_non_neuro_SAS_nhomalt gnomAD_exomes_non_neuro_nhomalt gnomAD_exomes_non_topmed_AC gnomAD_exomes_non_topmed_AF gnomAD_exomes_non_topmed_AFR_AC gnomAD_exomes_non_topmed_AFR_AF gnomAD_exomes_non_topmed_AFR_AN gnomAD_exomes_non_topmed_AFR_nhomalt gnomAD_exomes_non_topmed_AMR_AC gnomAD_exomes_non_topmed_AMR_AF gnomAD_exomes_non_topmed_AMR_AN gnomAD_exomes_non_topmed_AMR_nhomalt gnomAD_exomes_non_topmed_AN gnomAD_exomes_non_topmed_ASJ_AC gnomAD_exomes_non_topmed_ASJ_AF gnomAD_exomes_non_topmed_ASJ_AN gnomAD_exomes_non_topmed_ASJ_nhomalt gnomAD_exomes_non_topmed_EAS_AC gnomAD_exomes_non_topmed_EAS_AF gnomAD_exomes_non_topmed_EAS_AN gnomAD_exomes_non_topmed_EAS_nhomalt gnomAD_exomes_non_topmed_FIN_AC gnomAD_exomes_non_topmed_FIN_AF gnomAD_exomes_non_topmed_FIN_AN gnomAD_exomes_non_topmed_FIN_nhomalt gnomAD_exomes_non_topmed_NFE_AC gnomAD_exomes_non_topmed_NFE_AF gnomAD_exomes_non_topmed_NFE_AN gnomAD_exomes_non_topmed_NFE_nhomalt gnomAD_exomes_non_topmed_POPMAX_AC gnomAD_exomes_non_topmed_POPMAX_AF gnomAD_exomes_non_topmed_POPMAX_AN gnomAD_exomes_non_topmed_POPMAX_nhomalt gnomAD_exomes_non_topmed_SAS_AC gnomAD_exomes_non_topmed_SAS_AF gnomAD_exomes_non_topmed_SAS_AN gnomAD_exomes_non_topmed_SAS_nhomalt gnomAD_exomes_non_topmed_nhomalt gnomAD_genomes_AC gnomAD_genomes_AF gnomAD_genomes_AFR_AC gnomAD_genomes_AFR_AF gnomAD_genomes_AFR_AN gnomAD_genomes_AFR_nhomalt gnomAD_genomes_AMI_AC gnomAD_genomes_AMI_AF gnomAD_genomes_AMI_AN gnomAD_genomes_AMI_nhomalt gnomAD_genomes_AMR_AC gnomAD_genomes_AMR_AF gnomAD_genomes_AMR_AN gnomAD_genomes_AMR_nhomalt gnomAD_genomes_AN gnomAD_genomes_ASJ_AC gnomAD_genomes_ASJ_AF gnomAD_genomes_ASJ_AN gnomAD_genomes_ASJ_nhomalt gnomAD_genomes_EAS_AC gnomAD_genomes_EAS_AF gnomAD_genomes_EAS_AN gnomAD_genomes_EAS_nhomalt gnomAD_genomes_FIN_AC gnomAD_genomes_FIN_AF gnomAD_genomes_FIN_AN gnomAD_genomes_FIN_nhomalt gnomAD_genomes_MID_AC gnomAD_genomes_MID_AF gnomAD_genomes_MID_AN gnomAD_genomes_MID_nhomalt gnomAD_genomes_NFE_AC gnomAD_genomes_NFE_AF gnomAD_genomes_NFE_AN gnomAD_genomes_NFE_nhomalt gnomAD_genomes_POPMAX_AC gnomAD_genomes_POPMAX_AF gnomAD_genomes_POPMAX_AN gnomAD_genomes_POPMAX_nhomalt gnomAD_genomes_SAS_AC gnomAD_genomes_SAS_AF gnomAD_genomes_SAS_AN gnomAD_genomes_SAS_nhomalt gnomAD_genomes_controls_and_biobanks_AC gnomAD_genomes_controls_and_biobanks_AF gnomAD_genomes_controls_and_biobanks_AFR_AC gnomAD_genomes_controls_and_biobanks_AFR_AF gnomAD_genomes_controls_and_biobanks_AFR_AN gnomAD_genomes_controls_and_biobanks_AFR_nhomalt gnomAD_genomes_controls_and_biobanks_AMI_AC gnomAD_genomes_controls_and_biobanks_AMI_AF gnomAD_genomes_controls_and_biobanks_AMI_AN gnomAD_genomes_controls_and_biobanks_AMI_nhomalt gnomAD_genomes_controls_and_biobanks_AMR_AC gnomAD_genomes_controls_and_biobanks_AMR_AF gnomAD_genomes_controls_and_biobanks_AMR_AN gnomAD_genomes_controls_and_biobanks_AMR_nhomalt gnomAD_genomes_controls_and_biobanks_AN gnomAD_genomes_controls_and_biobanks_ASJ_AC gnomAD_genomes_controls_and_biobanks_ASJ_AF gnomAD_genomes_controls_and_biobanks_ASJ_AN gnomAD_genomes_controls_and_biobanks_ASJ_nhomalt gnomAD_genomes_controls_and_biobanks_EAS_AC gnomAD_genomes_controls_and_biobanks_EAS_AF gnomAD_genomes_controls_and_biobanks_EAS_AN gnomAD_genomes_controls_and_biobanks_EAS_nhomalt gnomAD_genomes_controls_and_biobanks_FIN_AC gnomAD_genomes_controls_and_biobanks_FIN_AF gnomAD_genomes_controls_and_biobanks_FIN_AN gnomAD_genomes_controls_and_biobanks_FIN_nhomalt gnomAD_genomes_controls_and_biobanks_MID_AC gnomAD_genomes_controls_and_biobanks_MID_AF gnomAD_genomes_controls_and_biobanks_MID_AN gnomAD_genomes_controls_and_biobanks_MID_nhomalt gnomAD_genomes_controls_and_biobanks_NFE_AC gnomAD_genomes_controls_and_biobanks_NFE_AF gnomAD_genomes_controls_and_biobanks_NFE_AN gnomAD_genomes_controls_and_biobanks_NFE_nhomalt gnomAD_genomes_controls_and_biobanks_SAS_AC gnomAD_genomes_controls_and_biobanks_SAS_AF gnomAD_genomes_controls_and_biobanks_SAS_AN gnomAD_genomes_controls_and_biobanks_SAS_nhomalt gnomAD_genomes_controls_and_biobanks_nhomalt gnomAD_genomes_flag gnomAD_genomes_nhomalt gnomAD_genomes_non_cancer_AC gnomAD_genomes_non_cancer_AF gnomAD_genomes_non_cancer_AFR_AC gnomAD_genomes_non_cancer_AFR_AF gnomAD_genomes_non_cancer_AFR_AN gnomAD_genomes_non_cancer_AFR_nhomalt gnomAD_genomes_non_cancer_AMI_AC gnomAD_genomes_non_cancer_AMI_AF gnomAD_genomes_non_cancer_AMI_AN gnomAD_genomes_non_cancer_AMI_nhomalt gnomAD_genomes_non_cancer_AMR_AC gnomAD_genomes_non_cancer_AMR_AF gnomAD_genomes_non_cancer_AMR_AN gnomAD_genomes_non_cancer_AMR_nhomalt gnomAD_genomes_non_cancer_AN gnomAD_genomes_non_cancer_ASJ_AC gnomAD_genomes_non_cancer_ASJ_AF gnomAD_genomes_non_cancer_ASJ_AN gnomAD_genomes_non_cancer_ASJ_nhomalt gnomAD_genomes_non_cancer_EAS_AC gnomAD_genomes_non_cancer_EAS_AF gnomAD_genomes_non_cancer_EAS_AN gnomAD_genomes_non_cancer_EAS_nhomalt gnomAD_genomes_non_cancer_FIN_AC gnomAD_genomes_non_cancer_FIN_AF gnomAD_genomes_non_cancer_FIN_AN gnomAD_genomes_non_cancer_FIN_nhomalt gnomAD_genomes_non_cancer_MID_AC gnomAD_genomes_non_cancer_MID_AF gnomAD_genomes_non_cancer_MID_AN gnomAD_genomes_non_cancer_MID_nhomalt gnomAD_genomes_non_cancer_NFE_AC gnomAD_genomes_non_cancer_NFE_AF gnomAD_genomes_non_cancer_NFE_AN gnomAD_genomes_non_cancer_NFE_nhomalt gnomAD_genomes_non_cancer_SAS_AC gnomAD_genomes_non_cancer_SAS_AF gnomAD_genomes_non_cancer_SAS_AN gnomAD_genomes_non_cancer_SAS_nhomalt gnomAD_genomes_non_cancer_nhomalt gnomAD_genomes_non_neuro_AC gnomAD_genomes_non_neuro_AF gnomAD_genomes_non_neuro_AFR_AC gnomAD_genomes_non_neuro_AFR_AF gnomAD_genomes_non_neuro_AFR_AN gnomAD_genomes_non_neuro_AFR_nhomalt gnomAD_genomes_non_neuro_AMI_AC gnomAD_genomes_non_neuro_AMI_AF gnomAD_genomes_non_neuro_AMI_AN gnomAD_genomes_non_neuro_AMI_nhomalt gnomAD_genomes_non_neuro_AMR_AC gnomAD_genomes_non_neuro_AMR_AF gnomAD_genomes_non_neuro_AMR_AN gnomAD_genomes_non_neuro_AMR_nhomalt gnomAD_genomes_non_neuro_AN gnomAD_genomes_non_neuro_ASJ_AC gnomAD_genomes_non_neuro_ASJ_AF gnomAD_genomes_non_neuro_ASJ_AN gnomAD_genomes_non_neuro_ASJ_nhomalt gnomAD_genomes_non_neuro_EAS_AC gnomAD_genomes_non_neuro_EAS_AF gnomAD_genomes_non_neuro_EAS_AN gnomAD_genomes_non_neuro_EAS_nhomalt gnomAD_genomes_non_neuro_FIN_AC gnomAD_genomes_non_neuro_FIN_AF gnomAD_genomes_non_neuro_FIN_AN gnomAD_genomes_non_neuro_FIN_nhomalt gnomAD_genomes_non_neuro_MID_AC gnomAD_genomes_non_neuro_MID_AF gnomAD_genomes_non_neuro_MID_AN gnomAD_genomes_non_neuro_MID_nhomalt gnomAD_genomes_non_neuro_NFE_AC gnomAD_genomes_non_neuro_NFE_AF gnomAD_genomes_non_neuro_NFE_AN gnomAD_genomes_non_neuro_NFE_nhomalt gnomAD_genomes_non_neuro_SAS_AC gnomAD_genomes_non_neuro_SAS_AF gnomAD_genomes_non_neuro_SAS_AN gnomAD_genomes_non_neuro_SAS_nhomalt gnomAD_genomes_non_neuro_nhomalt gnomAD_genomes_non_topmed_AC gnomAD_genomes_non_topmed_AF gnomAD_genomes_non_topmed_AFR_AC gnomAD_genomes_non_topmed_AFR_AF gnomAD_genomes_non_topmed_AFR_AN gnomAD_genomes_non_topmed_AFR_nhomalt gnomAD_genomes_non_topmed_AMI_AC gnomAD_genomes_non_topmed_AMI_AF gnomAD_genomes_non_topmed_AMI_AN gnomAD_genomes_non_topmed_AMI_nhomalt gnomAD_genomes_non_topmed_AMR_AC gnomAD_genomes_non_topmed_AMR_AF gnomAD_genomes_non_topmed_AMR_AN gnomAD_genomes_non_topmed_AMR_nhomalt gnomAD_genomes_non_topmed_AN gnomAD_genomes_non_topmed_ASJ_AC gnomAD_genomes_non_topmed_ASJ_AF gnomAD_genomes_non_topmed_ASJ_AN gnomAD_genomes_non_topmed_ASJ_nhomalt gnomAD_genomes_non_topmed_EAS_AC gnomAD_genomes_non_topmed_EAS_AF gnomAD_genomes_non_topmed_EAS_AN gnomAD_genomes_non_topmed_EAS_nhomalt gnomAD_genomes_non_topmed_FIN_AC gnomAD_genomes_non_topmed_FIN_AF gnomAD_genomes_non_topmed_FIN_AN gnomAD_genomes_non_topmed_FIN_nhomalt gnomAD_genomes_non_topmed_MID_AC gnomAD_genomes_non_topmed_MID_AF gnomAD_genomes_non_topmed_MID_AN gnomAD_genomes_non_topmed_MID_nhomalt gnomAD_genomes_non_topmed_NFE_AC gnomAD_genomes_non_topmed_NFE_AF gnomAD_genomes_non_topmed_NFE_AN gnomAD_genomes_non_topmed_NFE_nhomalt gnomAD_genomes_non_topmed_SAS_AC gnomAD_genomes_non_topmed_SAS_AF gnomAD_genomes_non_topmed_SAS_AN gnomAD_genomes_non_topmed_SAS_nhomalt gnomAD_genomes_non_topmed_nhomalt hg18_chr hg18_pos.1.based. hg19_chr hg19_pos.1.based. integrated_confidence_value integrated_fitCons_rankscore integrated_fitCons_score phastCons100way_vertebrate phastCons100way_vertebrate_rankscore phastCons17way_primate phastCons17way_primate_rankscore phastCons30way_mammalian phastCons30way_mammalian_rankscore phyloP100way_vertebrate phyloP100way_vertebrate_rankscore phyloP17way_primate phyloP17way_primate_rankscore phyloP30way_mammalian phyloP30way_mammalian_rankscore pos.1.based. ref refcodon rs_dbSNP Condel IntAct_feature_type IntAct_interaction_ac IntAct_interaction_ac.1 ClinVar.y