For more information, see gallia-core documentation, in particular the bioinformatics examples section.
sbt run
Uses Gallia transformations
to turn TSV rows such as:
#chr pos(1-based) ref alt aaref aaalt rs_dbSNP151 hg19_chr hg19_pos(1-based) hg18_chr hg18_pos(1-based) aapos 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 SIFT_score SIFT_converted_rankscore SIFT_pred SIFT4G_score SIFT4G_converted_rankscore SIFT4G_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 MetaSVM_score MetaSVM_rankscore MetaSVM_pred MetaLR_score MetaLR_rankscore MetaLR_pred Reliability_index M-CAP_score M-CAP_rankscore M-CAP_pred 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 Aloft_Fraction_transcripts_affected Aloft_prob_Tolerant Aloft_prob_Recessive Aloft_prob_Dominant Aloft_pred Aloft_Confidence 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-pred_coding Eigen-PC-raw_coding Eigen-PC-raw_coding_rankscore Eigen-PC-phred_coding 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 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_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 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 ExAC_nonTCGA_AC ExAC_nonTCGA_AF ExAC_nonTCGA_Adj_AC ExAC_nonTCGA_Adj_AF ExAC_nonTCGA_AFR_AC ExAC_nonTCGA_AFR_AF ExAC_nonTCGA_AMR_AC ExAC_nonTCGA_AMR_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_Adj_AC ExAC_nonpsych_Adj_AF ExAC_nonpsych_AFR_AC ExAC_nonpsych_AFR_AF ExAC_nonpsych_AMR_AC ExAC_nonpsych_AMR_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 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_exomes_controls_AC gnomAD_exomes_controls_AN gnomAD_exomes_controls_AF gnomAD_exomes_controls_nhomalt gnomAD_exomes_controls_AFR_AC gnomAD_exomes_controls_AFR_AN gnomAD_exomes_controls_AFR_AF gnomAD_exomes_controls_AFR_nhomalt gnomAD_exomes_controls_AMR_AC gnomAD_exomes_controls_AMR_AN gnomAD_exomes_controls_AMR_AF gnomAD_exomes_controls_AMR_nhomalt gnomAD_exomes_controls_ASJ_AC gnomAD_exomes_controls_ASJ_AN gnomAD_exomes_controls_ASJ_AF gnomAD_exomes_controls_ASJ_nhomalt gnomAD_exomes_controls_EAS_AC gnomAD_exomes_controls_EAS_AN gnomAD_exomes_controls_EAS_AF gnomAD_exomes_controls_EAS_nhomalt gnomAD_exomes_controls_FIN_AC gnomAD_exomes_controls_FIN_AN gnomAD_exomes_controls_FIN_AF gnomAD_exomes_controls_FIN_nhomalt gnomAD_exomes_controls_NFE_AC gnomAD_exomes_controls_NFE_AN gnomAD_exomes_controls_NFE_AF gnomAD_exomes_controls_NFE_nhomalt gnomAD_exomes_controls_SAS_AC gnomAD_exomes_controls_SAS_AN gnomAD_exomes_controls_SAS_AF gnomAD_exomes_controls_SAS_nhomalt gnomAD_exomes_controls_POPMAX_AC gnomAD_exomes_controls_POPMAX_AN gnomAD_exomes_controls_POPMAX_AF gnomAD_exomes_controls_POPMAX_nhomalt gnomAD_genomes_flag 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 gnomAD_genomes_controls_AC gnomAD_genomes_controls_AN gnomAD_genomes_controls_AF gnomAD_genomes_controls_nhomalt gnomAD_genomes_controls_AFR_AC gnomAD_genomes_controls_AFR_AN gnomAD_genomes_controls_AFR_AF gnomAD_genomes_controls_AFR_nhomalt gnomAD_genomes_controls_AMR_AC gnomAD_genomes_controls_AMR_AN gnomAD_genomes_controls_AMR_AF gnomAD_genomes_controls_AMR_nhomalt gnomAD_genomes_controls_ASJ_AC gnomAD_genomes_controls_ASJ_AN gnomAD_genomes_controls_ASJ_AF gnomAD_genomes_controls_ASJ_nhomalt gnomAD_genomes_controls_EAS_AC gnomAD_genomes_controls_EAS_AN gnomAD_genomes_controls_EAS_AF gnomAD_genomes_controls_EAS_nhomalt gnomAD_genomes_controls_FIN_AC gnomAD_genomes_controls_FIN_AN gnomAD_genomes_controls_FIN_AF gnomAD_genomes_controls_FIN_nhomalt gnomAD_genomes_controls_NFE_AC gnomAD_genomes_controls_NFE_AN gnomAD_genomes_controls_NFE_AF gnomAD_genomes_controls_NFE_nhomalt gnomAD_genomes_controls_POPMAX_AC gnomAD_genomes_controls_POPMAX_AN gnomAD_genomes_controls_POPMAX_AF gnomAD_genomes_controls_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 GTEx_V7_gene GTEx_V7_tissue Geuvadis_eQTL_target_gene
21 6445558 T A X C . 21 44473990 21 43347059 552;552;552;552;566 CBSL ENSG00000274276;ENSG00000274276;ENSG00000274276;ENSG00000274276;ENSG00000274276 ENST00000624406;ENST00000398168;ENST00000618024;ENST00000617706;ENST00000624934 ENSP00000485669;ENSP00000381234;ENSP00000479559;ENSP00000481719;ENSP00000485527 P0DN79;P0DN79;P0DN79;P0DN79;. CBSL_HUMAN;CBSL_HUMAN;CBSL_HUMAN;CBSL_HUMAN;. c.1656A>T;c.1656A>T;c.1656A>T;c.1656A>T;c.1698A>T p.X552C;p.X552C;p.X552C;p.X552C;p.X566C c.1656A>T;c.1656A>T;c.1656A>T;c.1656A>T;c.1698A>T p.Ter552Cysext*?;p.Ter552Cysext*?;p.Ter552Cysext*?;p.Ter552Cysext*?;p.Ter566Cysext*? c.1656A>T;c.1656A>T;c.1656A>T;c.1656A>T;c.1698A>T p.Ter552CysextTer31;p.Ter552CysextTer31;p.Ter552CysextTer14;p.Ter552CysextTer31;p.Ter566CysextTer31 principal2;principal2;principal2;principal2;alternative2 Y;Y;Y;Y;Y 1;1;1;1;5 .;.;.;YES;. - TGA 3 0 . T/T T/T T/T .;.;.;.;. . .;.;.;.;. .;.;.;.;. . .;.;.;.;. . . . . 1;1;1;1;1;1;1;1;1;1;1;1 0.08975 N;N;N;N;N;N;N;N;N;N;N;N complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae *464C;*566C;*552C;*552C;*552C;*552C;*464C;*552C;*552C;*552C;*552C;*566C .;.;.;.;. . .;.;.;.;. . . . .;.;.;.;. . .;.;.;.;. . . . . . . . . . . . . . . . .;.;.;.;. . .;.;.;.;. . . . . .;.;.;.;. . .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. 0.54113587345593983 0.05073 0.08502 0.14423 N AEFDBHCI . . . 0.200976666004101 0.51248 3.307481 -0.163821194829558 0.32880 1.875051 0.262962 0.04601 0 0.304816 0.05638 0 0.189914 0.04498 0 0.285054 0.05467 0 4.87 2.51 0.29435 0.223000 0.17501 -0.254000 0.08183 0.455000 0.21489 0.000000 0.06391 0.000000 0.01923 0.009000 0.08673 0.0:0.2717:0.0:0.7283 7.5162 0.26770 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .;.;.;.;. . . .
into objects like:
{
"shorthand": "21:44473990;T>A",
"locus": {
"hg20": {
"chromosome": "21",
"position": 6445558 },
"hg19": {
"chromosome": "21",
"position": 44473990 },
"hg18": {
"chromosome": "21",
"position": 43347059 },
"cds": { "strand": "-" } },
"genes": [
{
"AA_position": 552,
"symbol": "CBSL",
"APPRIS": "principal2",
"TSL": "tsl1",
"accession": "P0DN79",
"codon": {
"degeneracy": 0,
"ref": "TGA" },
"ensembl": {
"gene_id": "ENSG00000274276",
"transcript_id": "ENST00000624406",
"protein_id": "ENSP00000485669" },
"GENCODE": { "basic": "Y" },
"HGVS": {
"c": {
"ANNOVAR": "c.1656A>T",
"VEP": "c.1656A>T",
"snpEff": "c.1656A>T" },
"p": {
"ANNOVAR": "p.X552C",
"VEP": "p.Ter552CysextTer31",
"snpEff": "p.Ter552Cysext*?" } },
"Uniprot": {
"entry": "CBSL_HUMAN" } },
{ "AA_position": 552,
"symbol": "CBSL",
"APPRIS": "principal2",
"TSL": "tsl1",
"accession": "P0DN79",
"codon": {
"degeneracy": 0,
"ref": "TGA" },
"ensembl": {
"gene_id": "ENSG00000274276",
"transcript_id": "ENST00000398168",
"protein_id": "ENSP00000381234" },
"GENCODE": {
"basic": "Y" },
"HGVS": {
"c": {
"ANNOVAR": "c.1656A>T",
"VEP": "c.1656A>T",
"snpEff": "c.1656A>T" },
"p": {
"ANNOVAR": "p.X552C",
"VEP": "p.Ter552CysextTer31",
"snpEff": "p.Ter552Cysext*?" } },
"Uniprot": {
"entry": "CBSL_HUMAN" } },
{ "AA_position": 552,
"symbol": "CBSL",
"APPRIS": "principal2",
"TSL": "tsl1",
"accession": "P0DN79",
"codon": {
"degeneracy": 0,
"ref": "TGA" },
"ensembl": {
"gene_id": "ENSG00000274276",
"transcript_id": "ENST00000618024",
"protein_id": "ENSP00000479559" },
"GENCODE": {
"basic": "Y" },
"HGVS": {
"c": {
"ANNOVAR": "c.1656A>T",
"VEP": "c.1656A>T",
"snpEff": "c.1656A>T" },
"p": {
"ANNOVAR": "p.X552C",
"VEP": "p.Ter552CysextTer14",
"snpEff": "p.Ter552Cysext*?" } },
"Uniprot": {
"entry": "CBSL_HUMAN" } },
{ "AA_position": 552,
"symbol": "CBSL",
"APPRIS": "principal2",
"TSL": "tsl1",
"accession": "P0DN79",
"VEP_canonical": true,
"codon": {
"degeneracy": 0,
"ref": "TGA" },
"ensembl": {
"gene_id": "ENSG00000274276",
"transcript_id": "ENST00000617706",
"protein_id": "ENSP00000481719" },
"GENCODE": {
"basic": "Y" },
"HGVS": {
"c": {
"ANNOVAR": "c.1656A>T",
"VEP": "c.1656A>T",
"snpEff": "c.1656A>T" },
"p": {
"ANNOVAR": "p.X552C",
"VEP": "p.Ter552CysextTer31",
"snpEff": "p.Ter552Cysext*?" } },
"Uniprot": {
"entry": "CBSL_HUMAN" } },
{ "AA_position": 566,
"symbol": "CBSL",
"APPRIS": "alternative2",
"TSL": "tsl5",
"codon": {
"degeneracy": 0,
"ref": "TGA" },
"ensembl": {
"gene_id": "ENSG00000274276",
"transcript_id": "ENST00000624934",
"protein_id": "ENSP00000485527" },
"GENCODE": {
"basic": "Y" },
"HGVS": {
"c": {
"ANNOVAR": "c.1698A>T",
"VEP": "c.1698A>T",
"snpEff": "c.1698A>T" },
"p": {
"ANNOVAR": "p.X566C",
"VEP": "p.Ter566CysextTer31",
"snpEff": "p.Ter566Cysext*?"
}
}
}
],
"codon_position": 3,
"AA": {
"ref": "X",
"alt": "C" },
"rankscores": {
"MutationTaster": {
"converted": 0.08975 },
"DANN": {
"raw": 0.05073 },
"fathmm-MKL": {
"coding": {
"raw": 0.14423 } },
"Eigen": {
"coding": {
"full": {
"raw": {
"raw": 0.51248 } },
"PC": {
"raw": {
"raw": 0.3288 } } } },
"integrated": {
"fitCons": {
"raw": 0.04601 } },
"GM12878": {
"fitCons": {
"raw": 0.05638 } },
"H1-hESC": {
"fitCons": {
"raw": 0.04498 } },
"HUVEC": {
"fitCons": {
"raw": 0.05467 } },
"GERP++": {
"RS": {
"raw": 0.29435 } },
"phyloP100way": {
"vertebrate": {
"raw": 0.17501 } },
"phyloP30way": {
"mammalian": {
"raw": 0.08183 } },
"phyloP17way": {
"primate": {
"raw": 0.21489 } },
"phastCons100way": {
"vertebrate": {
"raw": 0.06391 } },
"phastCons30way": {
"mammalian": {
"raw": 0.01923 } },
"phastCons17way": {
"primate": {
"raw": 0.08673 } },
"SiPhy": {
"29way": {
"logOdds": {
"raw": 0.2677 } } } },
"DANN": {
"score": 0.5411358734559398 },
"fathmm-MKL": {
"coding": {
"score": 0.08502,
"group": "AEFDBHCI" } },
"FATHMM-MKL": {
"coding": {
"prediction": "N" } },
"Eigen": {
"coding": {
"full": {
"raw": {
"score": 0.200976666004101 },
"phred": 3.307481 },
"PC": {
"raw": {
"score": -0.163821194829558 },
"phred": 1.875051 } } },
"integrated": {
"fitCons": {
"score": 0.262962 },
"confidence": 0 },
"GM12878": {
"fitCons": {
"score": 0.304816 },
"confidence": 0 },
"H1-hESC": {
"fitCons": {
"score": 0.189914 },
"confidence": 0 },
"HUVEC": {
"fitCons": {
"score": 0.285054 },
"confidence": 0 },
"GERP++": {
"NR": 4.87,
"RS": {
"score": 2.51 } },
"phyloP": {
"100way": {
"vertebrate": 0.223 },
"30way": {
"mammalian": -0.254 },
"17way": {
"primate": {
"value": 0.455 } } },
"phastCons": {
"100way": {
"vertebrate": "0.000000" },
"30way": {
"mammalian": "0.000000" },
"17way": {
"primate": {
"value": "0.009000" } } },
"SiPhy": {
"29way": {
"pi": [
0,
0.2717,
0,
0.7283 ],
"logOdds": {
"score": 7.5162 } } },
"genotypes": {
"AltaiNeandertal": "T/T",
"Denisova": "T/T",
"VindijiaNeandertal": "T/T" },
"MutationTaster": [
{ "score": 1,
"AA_exchange": "*464C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*566C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*464C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*552C",
"model": "complex_aae",
"prediction": "N" },
{ "score": 1,
"AA_exchange": "*566C",
"model": "complex_aae",
"prediction": "N" }
]
}- Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutation. 32:894-899.
- Liu X, Jian X, and Boerwinkle E. 2013. dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations. Human Mutation. 34:E2393-E2402.
- Liu X, Wu C, Li C, and Boerwinkle E. 2016. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs. Human Mutation. 37:235-241.
- Liu X, Li C, Mou C, Dong Y, and Tu Y. 2020. dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome Medicine. 12:103.
- Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K* and Liu X*. (2015) Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Human Molecular Genetics 24(8):2125-2137. *corresponding authors [PDF]