Variants were annotated using annotation data from Tuberculist [ 38].
Variants were annotated using a custom annotation pipeline adding the following annotation for each detected variant: annotation with known polymorphism data from dbSNP130, genomic feature annotation (e.g., exon and intron), amino acid translations, and PhyloP conservation score (based on conservation of 44 vertebrate species) [Hoischen et al., 2010; Vissers et al., 2010].
Filtered variants were annotated by the Glu Genetics annotation pipeline [ 51].
Variants were annotated against the UCSC KnownGene annotation, dbSNP132, and the May 2011 release of the 1000 Genomes Project using ANNOVAR.
The variants were annotated using the popular variant annotation toolkit ANNOVAR (15).
Variants were annotated with the Ambry Variant Analyzer, a proprietary alignment and variant annotation software (Ambry Genetics).
Variants were annotated with overlapping genes, cytoband, gene region (Exonic, Intronic, Promoter, 5′UTR, 3′UTR, Splice Site), translational impact (if applicable), SIFT function prediction (if applicable), SIFT score (if applicable), dbSNP ID (if applicable) and frequency in the 1000 Genomes as well as frequency in the Complete Genomics Public Genome dataset.
Variants were annotated using Oncotator.
The variants were annotated using Annovar.
All variants were annotated against the Ensembl database.
Variants were annotated using Variant Effects Predictor version 2.8 [ 27].
