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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%).