Download Packages RVTESTS Description Fast, handy association test software for family/unrelated studies and quantitative/binary trait. Single variant test (score test, Wald test), burden tests (CMC, SKAT, VT) are implemented. It also facilitate meta-analysis. Software Package rvtests checkVCF Description Validation software for VCF file (used in lipid consortium) Software Package checkVCF SEQMINER Description Fast annotation software, and efficiently load and process VCF files. This software is integrated into EPACTS Software Package seqMiner QPLOT Description Quality check and visualize sequence alignment files Software Package QPLOT LASER Description Ancestry inference using off-target reads (suitable for target/exome sequencing) Software Package LASER Polymutt Description Family-based genotype caller Software Package Polymutt KARMA Description Illumina and ABI SOLiD sequence reads aligner Software Package karma ThunderVCF Description Low-coverage genotype calling using Hidden Markov-chain Model (HMM) Software Package Developing VAMPr Description To facilitate understanding of the connections between DNA variation and phenotypic AMR, we developed VAMPr (variant mapping and prediction of antibiotic resistance). It utilized 3,393 sequenced bacterial isolates from 9 species along with AMR phenotypes for 29 antibiotics following the Clinical & Laboratory Standards Institute (CLSI) guidelines. It also detected 14,615 variant genotypes and provided 93 association and prediction models. Website https://cdc.biohpc.swmed.edu/VAMPr/VAMPr.cgi Bayesian Integrative Model Description A Bayesian model for the integrative analysis of microbiome data Website https://shuangj00.github.io/IntegrativeBayes/articles/Tutorial.html FMAP Description Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies Website https://qbrc.swmed.edu/FMAP/