Closed alkc closed 5 months ago
This PR is just material for discussion at today's WGS meeting
Additions to consequence severity ranking:
my %rank = ( 'transcript_ablation' => 1, 'initiator_codon_variant' => 2, 'frameshift_variant' => 3, 'stop_gained' => 4, 'start_lost' => 5, 'stop_lost' => 6, 'splice_acceptor_variant' => 7, 'splice_donor_variant' => 8, 'inframe_deletion' => 9, 'transcript_amplification' => 10, 'splice_donor_5th_base_variant' => 11, <----------------- 'splice_region_variant' => 12, 'splice_donor_region_variant' => 13, <-------------------- 'splice_polypyrimidine_tract_variant' => 14, <----------- 'missense_variant' => 15, 'protein_altering_variant' => 16, 'inframe_insertion' => 17, 'incomplete_terminal_codon_variant' => 18, 'non_coding_transcript_exon_variant' => 19, 'synonymous_variant' => 20, 'mature_mirna_variant' => 21, 'non_coding_transcript_variant' => 22, 'regulatory_region_variant' => 23, 'upstream_gene_variant' => 24, 'regulatory_region_amplification' => 25, 'tfbs_amplification' => 26, '5_prime_utr_variant' => 27, 'intron_variant' => 28, '3_prime_utr_variant' => 29, 'feature_truncation' => 30, 'coding_transcript_variant' => 31, <--------------------- 'tf_binding_site_variant' => 32, 'start_retained_variant' => 33, 'stop_retained_variant' => 34, 'feature_elongation' => 35, 'regulatory_region_ablation' => 36, 'tfbs_ablation' => 37, 'coding_sequence_variant' => 38, 'downstream_gene_variant' => 39, 'nmd_transcript_variant' => 40, 'intergenic_variant' => 41, 'sequence_variant' => 42 <----------------------------- );
This PR is just material for discussion at today's WGS meeting
Additions to consequence severity ranking: