search

WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
234 stars 359 forks source link

PolyPhen and CADD annotations not available. #179

Closed kruthikaiyer0990 closed 2 years ago

kruthikaiyer0990 commented 2 years ago

Hi!

I downloaded the dbnsfp42c database for GRCh38 build. However, PolyPhen2 HDIV/HVAR and CADD scores/predictions are not available. Here's the header from hg38_dbnsfp42c

zcat hg38_dbnsfp42c.txt.gz | head 

#Chr    Start   End Ref Alt SIFT_score  SIFT_converted_rankscore    SIFT_pred   SIFT4G_score    SIFT4G_converted_rankscore  SIFT4G_pred LRT_score   LRT_converted_rankscore LRT_pred    MutationTaster_score    MutationTaster_converted_rankscore  MutationTaster_pred 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 MetaRNN_score   MetaRNN_rankscore   MetaRNN_pred    M-CAP_score M-CAP_rankscore M-CAP_pred  MutPred_score   MutPred_rankscore   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_pred  Aloft_Confidence    DANN_score  DANN_rankscore  fathmm-MKL_coding_score fathmm-MKL_coding_rankscore fathmm-MKL_coding_pred  fathmm-XF_coding_score  fathmm-XF_coding_rankscore  fathmm-XF_coding_pred   Eigen-raw_coding    Eigen-raw_coding_rankscore  Eigen-PC-raw_coding Eigen-PC-raw_coding_rankscore   integrated_fitCons_score    integrated_fitCons_rankscore    integrated_confidence_value GERP++_NR   GERP++_RS   GERP++_RS_rankscore phyloP100way_vertebrate phyloP100way_vertebrate_rankscore   phyloP30way_mammalian   phyloP30way_mammalian_rankscore phastCons100way_vertebrate  phastCons100way_vertebrate_rankscore    phastCons30way_mammalian    phastCons30way_mammalian_rankscore  SiPhy_29way_logOdds SiPhy_29way_logOdds_rankscore   Interpro_domain GTEx_V8_gene    GTEx_V8_tissue
kruthikaiyer0990 commented 2 years ago

I realized that c is commercial use and not all annotations are available for non-academic usage