VS-885 - Fix VAT TSV #8286
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VS-885 - Fix VAT TSV #8286
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8286 +/- ##
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Coverage ? 86.096%
Complexity ? 35609
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Files ? 2197
Lines ? 167119
Branches ? 18006
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Hits ? 143882
Misses ? 16802
Partials ? 6435 |
RoriCremer
approved these changes
Apr 12, 2023
RoriCremer
reviewed
Apr 12, 2023
| @@ -239,7 +239,8 @@ task MergeVatTSVs { | |||
| done | |||
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| echo_date "making header.gz" | |||
| echo "vid transcript contig position ref_allele alt_allele gvs_all_ac gvs_all_an gvs_all_af gvs_all_sc gvs_max_af gvs_max_ac gvs_max_an gvs_max_sc gvs_max_subpop gvs_afr_ac gvs_afr_an gvs_afr_af gvs_afr_sc gvs_amr_ac gvs_amr_an gvs_amr_af gvs_amr_sc gvs_eas_ac gvs_eas_an gvs_eas_af gvs_eas_sc gvs_eur_ac gvs_eur_an gvs_eur_af gvs_eur_sc gvs_mid_ac gvs_mid_an gvs_mid_af gvs_mid_sc gvs_oth_ac gvs_oth_an gvs_oth_af gvs_oth_sc gvs_sas_ac gvs_sas_an gvs_sas_af gvs_sas_sc gene_symbol transcript_source aa_change consequence dna_change_in_transcript variant_type exon_number intron_number genomic_location dbsnp_rsid gene_id gene_omim_id is_canonical_transcript gnomad_all_af gnomad_all_ac gnomad_all_an gnomad_failed_filter gnomad_max_af gnomad_max_ac gnomad_max_an gnomad_max_subpop gnomad_afr_ac gnomad_afr_an gnomad_afr_af gnomad_amr_ac gnomad_amr_an gnomad_amr_af gnomad_asj_ac gnomad_asj_an gnomad_asj_af gnomad_eas_ac gnomad_eas_an gnomad_eas_af gnomad_fin_ac gnomad_fin_an gnomad_fin_af gnomad_nfr_ac gnomad_nfr_an gnomad_nfr_af gnomad_sas_ac gnomad_sas_an gnomad_sas_af gnomad_oth_ac gnomad_oth_an gnomad_oth_af revel splice_ai_acceptor_gain_score splice_ai_acceptor_gain_distance splice_ai_acceptor_loss_score splice_ai_acceptor_loss_distance splice_ai_donor_gain_score splice_ai_donor_gain_distance splice_ai_donor_loss_score splice_ai_donor_loss_distance omim_phenotypes_id omim_phenotypes_name clinvar_classification clinvar_last_updated clinvar_phenotype" | gzip > header.gz | |||
| # NOTE: Contents of tsvs exported from BigQuery are tab-separated, the header must also be tab-separated! | |||
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VS-885: Fix the header of the VAT TSV to use tab character