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rvtests - Rare variant test software for next generation sequencing data

  •    C++

Rvtests, which stands for Rare Variant tests, is a flexible software package for genetic association analysis for sequence datasets. Since its inception, rvtests was developed as a comprehensive tool to support genetic association analysis and meta-analysis. It can analyze both unrelated individual and related (family-based) individuals for both quantitative and binary outcomes. It includes a variety of association tests (e.g. single variant score test, burden test, variable threshold test, SKAT test, fast linear mixed model score test). It takes VCF/BGEN/PLINK format as genotype input file and takes PLINK format phenotype file and covariate file. With new implementation of the BOLT-LMM/MINQUE algorithm as well as a series of software engineering optimizations, our software package is capable of analyzing datasets of up to 1,000,000 individuals in linear mixed models on a computer workstation, which makes our tool one of the very few options for analyzing large biobank scale datasets, such as UK Biobank. RVTESTS supports both single variant and gene-level tests. It also allows for highly effcient generation of covariance matrices between score statistics in RAREMETAL format, which can be used to support the next wave of meta-analysis that incorporates large biobank datasets.

peddy - genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

  •    Jupyter

peddy compares familial-relationships and sexes as reported in a PED/FAM file with those inferred from a VCF. It samples the VCF at about 25000 sites (plus chrX) to accurately estimate relatedness, IBS0, heterozygosity, sex and ancestry. It uses 2504 thousand genome samples as backgrounds to calibrate the relatedness calculation and to make ancestry predictions.

svtyper - Bayesian genotyper for structural variants

  •    Python

SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data. Users must supply a VCF file of sites to genotype (which may be generated by LUMPY) as well as a BAM/CRAM file of Illumina paired-end reads aligned with BWA-MEM. SVTyper assesses discordant and concordant reads from paired-end and split-read alignments to infer genotypes at each site. Algorithm details and benchmarking are described in Chiang et al., 2015. svtyper depends on pysam (version 0.15.0 or newer), numpy, and scipy; svtyper-sso additionally depends on cytoolz. If the dependencies aren't already available on your system, pip will attempt to download and install them.

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