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%). |