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join_variant_summary_with_clinvar_alleles.py
generates clinvar_alleles_combined.multi.tsv.gz by joining clinvar_alleles_grouped.multi.tsv.gz to variant_summary.txt.gz
using allele_id as the join key.
While doing this, it switches the clinical_significance column to the value from variant_summary.txt.gz (but doesn't update the clinical_significance_ordered column), so the values differ between the .xml release and variant_summary.txt.gz
I wonder if we should set these as 'conflicting interpretation' in both clinical_significance and clinical_significance_ordered columns?
This is the result of join_data.R for multi
It's wrong: NM_002977.3(SCN9A):c.[2794A>C;2971G>T] – Haplotype
Looking at each step:
clinvar_table_raw.multi.tsv - Correct
clinvar_table_normalized.multi.tsv.gz - Correct
clinvar_allele_trait_pairs.multi.tsv.gz - Correct
clinvar_alleles_grouped.multi.tsv.gz - Correct
clinvar_alleles_combined.multi.tsv.gz - WRONG
There are 20 halpotype variants with this same issue:
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