Why do only some variants get splicing scores?

Help & Support
1

I ran this loop on 91 variants. All variants get RNA_SEQ outputs but only 6 variants got SPLICE_SITES, SPLICE_SITE_USAGE, SPLICE_JUNCTION scores. Why might that be?

results = [] 
for i, variant in tqdm(df_gene.iterrows(), total=len(df_gene)): 

variant = genome.Variant( chromosome='chr'+str(variant['#CHROM']), position=int(variant['POS']), reference_bases=variant['REF'], alternate_bases=variant['ALT'], name=variant['ID'], ) 

interval = variant.reference_interval.resize(dna_client.SUPPORTED_SEQUENCE_LENGTHS['SEQUENCE_LENGTH_1MB']) 

variant_scores = model.score_variant( interval=interval, variant=variant, variant_scorers=list(variant_scorers.RECOMMENDED_VARIANT_SCORERS.values()), organism=dna_client.Organism.HOMO_SAPIENS, ) 

results.append(variant_scores)
2

Hi There!

Thanks for reaching out.

The reason you are seeing splicing scores for only 6 out of the 91 variants is because the splicing scorers (SPLICE_SITES, SPLICE_SITE_USAGE, and SPLICE_JUNCTIONS) only evaluate and return outputs for genes that directly overlap with the position of the variant.

In contrast, the RNA_SEQ scorer evaluates and considers all genes present within the entire 1 Mb interval, regardless of whether they overlap with the variant itself.

Kind regards,
Tumi