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modify clinvar star assignment for no interpretation variants #139

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Aug 22, 2023
Merged

modify clinvar star assignment for no interpretation variants #139

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de0390a
modify clinvar star assignment for no interpretation variants
Aug 22, 2023
ea91889
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rjcorb Aug 22, 2023
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modify clinvar star assignment for no interpretation variants
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rjcorb committed Aug 22, 2023
commit de0390acced5c38a81c93d2ef0b035827d658365
4 changes: 2 additions & 2 deletions AutoGVP/01-annotate_variants_CAVATICA_input.R
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Original file line number Diff line number Diff line change
Expand Up @@ -160,7 +160,7 @@ clinvar_anno_vcf_df <- clinvar_anno_vcf_df %>%
str_detect(INFO, "CLNREVSTAT\\=reviewed_by_expert_panel") ~ "3",
str_detect(INFO, "CLNREVSTAT\\=practice_guideline") ~ "4",
str_detect(INFO, "CLNREVSTAT\\=criteria_provided,_conflicting_interpretations") ~ "1NR",
str_detect(INFO, "no_assertion") ~ "0",
str_detect(INFO, "no_assertion|no_interpretation") ~ "0",
TRUE ~ NA_character_
),
## extract the calls and put in own column
Expand Down Expand Up @@ -419,7 +419,7 @@ master_tab <- master_tab %>%
evidenceBP = coalesce(as.double(evidenceBP.x, evidenceBP.y)),
Intervar_evidence = coalesce(`InterVar: InterVar and Evidence.x`, `InterVar: InterVar and Evidence.y`),
# replace second final call with the second one because we did not use interVar results
final_call.x = if_else(Stars == "0", final_call.y, final_call.x)
final_call.x = if_else(Stars == "0" | is.na(Stars), final_call.y, final_call.x)
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good catch!

)

## combine final calls into one choosing the appropriate final call
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4 changes: 2 additions & 2 deletions AutoGVP/01-annotate_variants_custom_input.R
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Expand Up @@ -172,7 +172,7 @@ clinvar_anno_vcf_df <- vroom(input_clinVar_file, comment = "#", delim = "\t", co
str_detect(INFO, "CLNREVSTAT\\=reviewed_by_expert_panel") ~ "3",
str_detect(INFO, "CLNREVSTAT\\=practice_guideline") ~ "4",
str_detect(INFO, "CLNREVSTAT\\=criteria_provided,_conflicting_interpretations") ~ "1NR",
str_detect(INFO, "no_assertion") ~ "0",
str_detect(INFO, "no_assertion|no_interpretation") ~ "0",
TRUE ~ NA_character_
),
## extract the calls and put in own column
Expand Down Expand Up @@ -434,7 +434,7 @@ master_tab <- master_tab %>%
Intervar_evidence = coalesce(`InterVar: InterVar and Evidence.x`, `InterVar: InterVar and Evidence.y`),

# replace second final call with the first one because we did not use clinvar results
final_call.x = if_else(Stars == "0", final_call.y, final_call.x),
final_call.x = if_else(Stars == "0" | is.na(Stars), final_call.y, final_call.x),
)

## combine final calls into one choosing the appropriate final call
Expand Down
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