NHLBI Exome Sequencing Project (ESP) Exome Variant Server Home Data Browser Data Usage and Release How to Use What's New Contact and FAQ Downloads Data Usage We request that any use of data obtained from the NHLBI GO ESP Exome Variant Server be cited in publications. Citation Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA (URL: http://evs.gs.washington.edu/EVS/) [date (month, yr) accessed]. Acknowledgment for Publication The authors would like to thank the NHLBI GO Exome Sequencing Project and its ongoing studies which produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923), the WHI Sequencing Project (HL-102924), the Broad GO Sequencing Project (HL-102925), the Seattle GO Sequencing Project (HL-102926) and the Heart GO Sequencing Project (HL-103010). Public Data Release The current EVS data release (ESP6500SI-V2) is taken from 6503 samples drawn from multiple ESP cohorts and represents all of the ESP exome variant data. Sequences were aligned to NCBI build 37 human genome reference using BWA. PCR Duplicates were removed using Picard. Alignments were recalibrated using GATK. Lane-level indel realignments and base alignment quality (BAQ) adjustments were applied. All data were simultaneously analyzed for exome SNP variants at the University of Michigan (by the Abecasis Laboratory). SNPs were called using a two-step approach. First, genotype likelihood files (GLFs) were generated using samtools pileup on individual BAM files. Next, we used glfMultiples, a multi-sample variant caller, to generate initial SNP calls. Details of the likelihood model implemented in glfMultiples are given in Li et al (Genome Research (2011) 21:940-951; section entitled "Identifying Potential Polymorphic Sites"). The Michigan SNP calling pipeline is available at: http://genome.sph.umich.edu/wiki/UMAKE. This pipeline makes diploid calls for pseudo-autosomal regions of male samples and haploid calls for the rest of the chromosome. Female samples have diploid calls for all regions on the X chromosome. SNPs were filtered by a machine-learning technique called support vector machine (SVM) classification (for a detailed description, see Filter Status). Small INDEL variants were analyzed at the Broad Institute (by the Genome Sequencing and Analysis group) using the GATK variation discovery pipeline following the guidelines in the GATK best practices v4. More specifically, each BAM was reduced to create a Reduced BAM, and then INDELs were discovered by analyzing all samples simultaneously with the GATK UnifiedGenotyper, and subsequently filtered by the GATK Variant Quality Score Recalibration (VQSR) filtering model, again following the V4 best practices. The INDEL genotypes for the X and Y chromosomes were adjusted to be consistent with the samples' genders. Female samples have diploid calls for all regions on the X chromosome. Male samples have diploid calls for the pseudo-autosomal regions on the X chromosome and haploid calls for the rest of the X chromosome and on the Y chromosome as well. However, the INDEL calls for the ESP data are preliminary and not as robust as the SNP calls at this point, users are advised to keep this difference in mind when applying the ESP data to research studies. All SNPs and INDELs were further annotated by SeattleSeqAnnotation137, and the variant annotations at the coding-DNA and protein levels follow mostly the HGVS conventions. A subset of this data (ESP2500) that has more stringent filtering criteria is available in the latest release of dbSNP (build 134), and published by the ESP Population Genetics and Statistical Analysis Working Group. (publication) Terms of Service This web site is designed to disseminate exome sequencing data generated through federal funding from the NHLBI. This data is provided free-of-charge, provided the following permission statement is followed. There may be other information on the site, such as links to other sites, references to other project groups and federal grants. The University of Washington has no responsibility for these links and information. Permission The contents of the NHLBI ESP Exome Variant Server web site are intended for educational or research purposes. As stated above, a subset of exome variants on this website have been deposited in dbSNP, and the full dataset will be deposited in dbGaP as part of the ESP cohort data. We place no restrictions on the use of the data available from the EVS. You may download or copy the content and other downloadable items displayed on the Exome Variant Server portion of the web site, provided that in using the data, you follow the citation format given above. Privacy Terms