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diskin-lab-chop / AutoGVP

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Bug: ClinVar calls with conflicting interpretations have NA clinvar stars #148

Closed rjcorb closed 1 year ago

rjcorb commented 1 year ago

Provide the command used or report the bug here

Final output currently reports clinvar_stars == NA for all variants called by ClinVar but that have conflicting interpretations. For example: 

# A tibble: 18 × 16
   chr       start ref   alt         rs_id       gene_symbol_vep variant_classification_vep                            HGVSg HGVSc HGVSp autogvp_call autogvp_call_reason clinvar_stars clinvar_clinsig intervar_evidence gnomad_3_1_1_AF_non_…¹
   <chr>     <dbl> <chr> <chr>       <chr>       <chr>           <chr>                                                 <chr> <chr> <chr> <chr>        <chr>                       <dbl> <chr>           <chr>                              <dbl>
 1 chr1  241500602 T     TGAGA       rs144131869 FH              splice_polypyrimidine_tract_variant&intron_variant    chr1… c.12… NA    Uncertain_s… ClinVar                        NA Uncertain_sign… InterVar: Benign…             0         
 2 chr11   2168615 C     T           rs370429316 TH              synonymous_variant                                    chr1… c.36… p.Pr… Likely_beni… ClinVar                        NA Likely_benign   InterVar: Likely…             0.000386  
 3 chr11  77180470 C     T           rs781916427 MYO7A           missense_variant                                      chr1… c.26… p.Ar… Uncertain_s… ClinVar                        NA Uncertain_sign… InterVar: Uncert…             0.0000270 
 4 chr13  23320613 TTG   T           rs796860219 SGCG            intron_variant                                        chr1… c.57… NA    Uncertain_s… ClinVar                        NA Uncertain_sign… InterVar: Uncert…             0.000615  
 5 chr13  23365176 C     T           rs145681117 SACS            synonymous_variant                                    chr1… c.44… p.Al… Likely_beni… ClinVar                        NA Likely_benign   InterVar: Likely…             0.0000473 
 6 chr14  35402853 G     A           rs142195196 NFKBIA          missense_variant                                      chr1… c.55… p.Th… Uncertain_s… ClinVar                        NA Uncertain_sign… InterVar: Uncert…             0.000359  
 7 chr15  48489875 T     C           rs111801777 FBN1            missense_variant                                      chr1… c.30… p.Th… Likely_beni… ClinVar                        NA Likely_benign   InterVar: Uncert…             0.000324  
 8 chr15  48738644 T     C           rs200883218 CEP152          missense_variant                                      chr1… c.47… p.Th… Uncertain_s… ClinVar                        NA Uncertain_sign… InterVar: Uncert…             0.000304  
 9 chr15  98899624 A     G           rs55895813  IGF1R           splice_donor_region_variant&intron_variant            chr1… c.12… NA    Uncertain_s… ClinVar                        NA Uncertain_sign… InterVar: Uncert…             0.000514  
10 chr17  61483613 A     AGTGTGTGTGT rs149977669 TBX4            3_prime_UTR_variant                                   chr1… c.*1… NA    Benign       ClinVar                        NA Benign          InterVar: Benign…             0         
# ℹ abbreviated name: ¹​gnomad_3_1_1_AF_non_cancer

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