The variant call format provides efficient and robust storage of GWAS summary statistics
نویسندگان
چکیده
منابع مشابه
The variant call format and VCFtools
SUMMARY The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and ha...
متن کاملVCF-kit: assorted utilities for the variant call format
Summary The variant call format (VCF) is a popular standard for storing genetic variation data. As a result, a large collection of tools has been developed that perform diverse analyses using VCF files. However, some tasks common to statistical and population geneticists have not been created yet. To streamline these types of analyses, we created novel tools that analyze or annotate VCF files a...
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SeqArray - a storage-efficient high-performance data format for WGS variant calls
Motivation Whole-genome sequencing (WGS) data are being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a general text-based format developed to store variant genotypes and their annotations. However, VCF files are large and data retrieval is relatively slow. Here we introduce a ...
متن کاملEpigenome-wide association study and integrative analysis with the transcriptome based on GWAS summary statistics
The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants are still not fully understood. On the other hand, there is increasing interest in exploring the role of epigenetic variations such as DNA methylation in dise...
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ژورنال
عنوان ژورنال: Genome Biology
سال: 2021
ISSN: 1474-760X
DOI: 10.1186/s13059-020-02248-0