The Atlas2 Suite Pipeline. (a) The Atlas2 Suite is designed to accept as input single sample BAM files which are individually processed by Atlas-SNP2 and/or Atlas-Indel2 to produce single sample variant calls in VCF format. Both Atlas-SNP2 and Atlas-Indel2 use the same basic algorithm: for each variant site all the read data is compiled, the compiled data is fed into a logistic regression model for evaluation, and variants that are of sufficiently high quality and pass the heuristic filters are then genotyped and output as a VCF file. For population analysis, multiple single-sample VCF files may be combined into a population-level VCF with any missing coverage information filled in. (b) The Atlas2 Suite is available for use in both a command line version and through the Baylor College of Medicine (BCM) Genboree Server.