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Table 4 Pipeline elements and characteristics of successful CLARITY entries

From: An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

  Consensus (if any) Finalists Other tools used (% overall)
Mapping    
Read alignment Used supplied alignments (52%) Used supplied alignments (63%) Recomputed alignment data (48%)
Variant detection GATK and/or SAMtools (75%) GATK and/or SAMtools (75%) DNAnexus (5%), FreeBayes (5%), CGI variant table (5%), Avadis NGS (5%), LifeScope (5%)
Quality control metrics    
Annotation Annovar (52%) Annovar (63%) Online Mendelian Inheritance in Man (19%), Uniprot (5%), in-house software (5%), SeattleSeq (5%), Variant Tools (10%), KggSeq (5%), SNPedia (5%), ClinVar (5%), PharmGKB (5%), Ingenuity (10%), SG-ADVISER (5%), Human Gene Mutation Database (10%), Genome Trax (5%), dbNSFP (5%), VEP, in-house MapSNPs tool (5%), snpEFF (5%), Genomatix GeneGrid and CeGaT annotation pipeline (5%)
Clinical extraction Sift and/or Polyphen (90%) Sift and/or Polyphen (100%) MutationTaster (10%), LRT Omega, GERP, PhyloP, and FreeBayes (5%)
Validation    
Report generation Filter by relevance to phenotype (71%). Consult with clinician in relevant area (63%). Clinical summary geared towards: non-geneticist clinician (47%), clinical geneticist (29%). Filter by relevance to phenotype (100%). Consult with clinician in relevant area (100%). Clinical summary geared towards: non-geneticist clinician (38%), clinical geneticist (38%).