Additional file 1: of A hybrid computational strategy to address WGS variant analysis in >5000 samples

Figure S1. Venn Diagram of number of SNPs called by GATK-HC, GATK-UG, SNPTools and GotCloud and the FDR using HumanExome BeadChip array with 3533 shared samples as control. Figure S2. Rediscovery rate of SNP in the Exome region as function of alternate allele frequency using CHARGE WES variant call set as gold standard. The rediscovery rate exceeds 95% when alternate allele frequency f>=5x10-4 (AC>=5). Table S1. The choice of AWS instances used to deploy goSNAP for CHARGE WGS variant discovery in Stage A. All the jobs were scheduled via DNAnexus platform. Note that this list does not include the jobs for slicing and repacking in Stage A. Table S2. Instance specs in the “cost-effective” and “time-sensitive” mode of running goSNAP. Table S3. Profile of goSNAP runtime (in hour) with different region size, 100 Kbp and 1 Mbp, and different instance specifications. Table S4. Profile of GATK-UG runtime (in hour) with different region size, 100 Kbp and 1 Mbp, and different instance specifications. (DOCX 232 kb