Add missense raw score in the variant modal

[Char-Al]

It seems like a good idea for the user to have the score in the modal windows. I'll check how this can be achieved. I'm currently using VEP and dbnsfp for annotation.

I think all usefull scores are liste below, maybe we :

• Missense:
  • Rankscore :
  • [x] SIFT_converted_rankscore
  • [x] SIFT4G_converted_rankscore
  • [x] Polyphen2_HDIV_rankscore
  • [x] Polyphen2_HVAR_rankscore
  • [x] LRT_converted_rankscore
  • [x] MutationTaster_converted_rankscore
  • [x] MutationAssessor_rankscore
  • [x] FATHMM_converted_rankscore
  • [x] PROVEAN_converted_rankscore
  • [x] VEST4_rankscore
  • [x] MetaSVM_rankscore
  • [x] MetaLR_rankscore
  • [x] M-CAP_rankscore
  • [x] REVEL_rankscore
  • [x] MutPred_rankscore
  • [x] MVP_rankscore
  • [x] MPC_rankscore
  • [x] PrimateAI_rankscore
  • [x] DEOGEN2_rankscore
  • [x] BayesDel_addAF_rankscore
  • [x] BayesDel_noAF_rankscore
  • [x] ClinPred_rankscore
  • [x] LIST-S2_rankscore
  • [x] CADD_raw_rankscore
  • [x] CADD_raw_rankscore_hg19
  • [x] DANN_rankscore
  • [x] fathmm-MKL_coding_rankscore
  • [x] fathmm-XF_coding_rankscore
  • [x] Eigen-raw_coding_rankscore
  • [x] Eigen-PC-raw_coding_rankscore
  • [x] GenoCanyon_rankscore
  • [x] integrated_fitCons_rankscore
  • [x] GM12878_fitCons_rankscore
  • [x] H1-hESC_fitCons_rankscore
  • [x] HUVEC_fitCons_rankscore
  • [x] LINSIGHT_rankscore
  • rawscore :
  • [ ] SIFT_score
  • [ ] SIFT_pred
  • [ ] SIFT4G_score
  • [ ] SIFT4G_pred
  • [ ] Polyphen2_HDIV_score
  • [ ] Polyphen2_HDIV_pred
  • [ ] Polyphen2_HVAR_score
  • [ ] Polyphen2_HVAR_pred
  • [ ] LRT_score
  • [ ] LRT_pred
  • [ ] LRT_Omega
  • [ ] MutationTaster_score
  • [ ] MutationTaster_pred
  • [ ] MutationTaster_model
  • [ ] MutationTaster_AAE
  • [ ] MutationAssessor_score
  • [ ] MutationAssessor_pred
  • [ ] FATHMM_score
  • [ ] FATHMM_pred
  • [ ] PROVEAN_score
  • [ ] PROVEAN_pred
  • [ ] VEST4_score
  • [ ] MetaSVM_score
  • [ ] MetaSVM_pred
  • [ ] MetaLR_score
  • [ ] MetaLR_pred
  • [ ] Reliability_index
  • [ ] M-CAP_score
  • [ ] M-CAP_pred
  • [ ] REVEL_score
  • [ ] MutPred_score
  • [ ] MutPred_protID
  • [ ] MutPred_AAchange
  • [ ] MutPred_Top5features
  • [ ] MVP_score
  • [ ] MPC_score
  • [ ] PrimateAI_score
  • [ ] PrimateAI_pred
  • [ ] DEOGEN2_score
  • [ ] DEOGEN2_pred
  • [ ] BayesDel_addAF_score
  • [ ] BayesDel_addAF_pred
  • [ ] BayesDel_noAF_score
  • [ ] BayesDel_noAF_pred
  • [ ] ClinPred_score
  • [ ] ClinPred_pred
  • [ ] LIST-S2_score
  • [ ] LIST-S2_pred
  • [ ] Aloft_Fraction_transcripts_affected
  • [ ] Aloft_prob_Tolerant
  • [ ] Aloft_prob_Recessive
  • [ ] Aloft_prob_Dominant
  • [ ] Aloft_pred
  • [ ] Aloft_Confidence
  • [ ] CADD_raw
  • [ ] CADD_phred
  • [ ] CADD_raw_hg19
  • [ ] CADD_phred_hg19
  • [ ] DANN_score
  • [ ] fathmm-MKL_coding_score
  • [ ] fathmm-MKL_coding_pred
  • [ ] fathmm-MKL_coding_group
  • [ ] fathmm-XF_coding_score
  • [ ] fathmm-XF_coding_pred
  • [ ] Eigen-raw_coding
  • [ ] Eigen-phred_coding
  • [ ] Eigen-PC-raw_coding
  • [ ] Eigen-PC-phred_coding
  • [ ] GenoCanyon_score
  • [ ] integrated_fitCons_score
  • [ ] integrated_confidence_value
  • [ ] GM12878_fitCons_score
  • [ ] GM12878_confidence_value
  • [ ] H1-hESC_fitCons_score
  • [ ] H1-hESC_confidence_value
  • [ ] HUVEC_fitCons_score
  • [ ] HUVEC_confidence_value
  • [ ] LINSIGHT
• Conservation :
  • rankscore :
  • [x] GERP++_RS_rankscore
  • [x] phyloP100way_vertebrate_rankscore
  • [x] phyloP30way_mammalian_rankscore
  • [x] phyloP17way_primate_rankscore
  • [x] phastCons100way_vertebrate_rankscore
  • [x] phastCons30way_mammalian_rankscore
  • [x] phastCons17way_primate_rankscore
  • [x] SiPhy_29way_logOdds_rankscore
  • [x] bStatistic_converted_rankscore
  • rawscore :
  • [ ] GERP++_NR
  • [ ] GERP++_RS
  • [ ] phyloP100way_vertebrate
  • [ ] phyloP30way_mammalian
  • [ ] phyloP17way_primate
  • [ ] phastCons100way_vertebrate
  • [ ] phastCons30way_mammalian
  • [ ] phastCons17way_primate
  • [ ] SiPhy_29way_pi
  • [ ] SiPhy_29way_logOdds
  • [ ] bStatistic
• other :
  • [ ] refcodon
  • [ ] codonpos
  • [ ] codon_degeneracy
  • [ ] Ancestral_allele
  • [ ] AltaiNeandertal
  • [ ] Denisova
  • [ ] VindijiaNeandertal

[thomasguignard]

It could be nice to get at a glance something like the "top 10 most striking scores" as a summary/bigPicture of the variant, in another modal tab

[Char-Al]

Since I haven't annotated all the scores, I need to develop a function to reannotate all the variants in the current database.

• [ ] Convert variant in DB into VCF
• [ ] Annotate all variant
• [ ] Write it into DB

[Char-Al]

It could be nice to get at a glance something like the "top 10 most striking scores" as a summary/bigPicture of the variant, in another modal tab @thomasguignard

SEAL already includes a 'Top 10 Most Striking Scores' feature as part of its functionality. You can find this summary in the 'Missense' column on the main sample view. Additionally, you can view this representation within the 'Missense' modal, displayed as a radar chart.