Table 1.

Example Candidate List Annotations

Item Name	Annotation Sources*	Implementation Notes
Identifier (unique for each variant in candidate list)	Sequencing/Assembling/Genotyping Facility**, GATK
Chromosome Number	Sequencing/Assembling/Genotyping Facility**, GATK
Variant Position Within Chromosome	Sequencing/Assembling/Genotyping Facility**, GATK	Positions are given in the context of a specific reference genome, e.g. NCBI hg18/build36
Reference allele	Sequencing/Asembling/Genotyping Facility**, GATK
Variant allele	Sequencing/Asembling/Genotyping Facility**, GATK
Variant type (exon, intron, etc.)	Annovar, SeattleSeq, GATK, VAAST
Gene name	Annovar, SeattleSeq, GATK, VAAST
Transcript	Annovar, SeattleSeq, GATK, VAAST
Strand	Annovar, SeattleSeq, GATK, VAAST
Reference Amino Acid	Annovar, SeattleSeq, GATK, VAAST
Variant Amino Acid	Annovar, SeattleSeq, GATK, VAAST
Amino Acid Position	Annovar, SeattleSeq, GATK, VAAST
Pathogenicity Score	Galaxy, GATK, PolyPhen, many others	NISC provides “CDPred” score
Coverage	Samtools, Bed tools, GATK
Quality Measure	Samtools, GATK	NISC provides MPG and MPG/coverage scores. Quality scores should be calibrated to a specific sequencing center/source
Mendelian Consistency for various genetic models	Manual inspection with spreadsheet, VAR-MD, VAAST	NISC provides annotation with in-house software
Compound Heterozygote Pairing for Autosomal Recessive Genetic Model	Manual inspection with spreadsheet	NISC provides annotation with in-house software

^*These are incomplete lists. A broad and rapidly expanding list of tools is available.

^**Often a collaborating sequencing facility can provide some or all of the annotations listed here. Most of the annotations can be carried out separately if needed. However, synergistic benefits can accrue if assembling and genotyping are performed by the same team.