CAPICE is a computational method for predicting the pathogenicity of SNVs and InDels. It is a gradient boosting tree model trained using a variety of genomic annotations used by CADD score and trained on the clinical significance. CAPICE performs consistently across diverse independent synthetic, and real clinical data sets. It ourperforms the current best method in pathogenicity estimation for variants of different molecular consequences and allele frequency.

The software can be used as web service, as pre-computed scores or by installing the software locally, all described below.

CAPICE can be used as online service as part of VIP at https://vip.molgeniscloud.org

• VEP v111
  • Including VEP cache (which needs to be unarchived!):
    • homo_sapiens_refseq_vep_107_GRCh38
  • Including plugin(s):
    • Grantham
    • SpliceAI
  • Including additional data (GRCh38) available here:
    • Gnomad v4 including index file.
    • hg38.phyloP100way.bw
    • spliceai_scores.masked.indel.hg38.vcf.gz
    • spliceai_scores.masked.indel.hg38.vcf.gz.tbi
    • spliceai_scores.masked.snv.hg38.vcf.gz
    • spliceai_scores.masked.snv.hg38.vcf.gz.tbi
• Apptainer == 1.1.* (For: BCFTools singularity image).
  • Singularity could also work, but requires manual adjusting of the conversion script.
• Python >=3.10