{"repo":"KalinNonchev/gnomAD_DB","free":true,"listed":false,"github":"https://github.com/KalinNonchev/gnomAD_DB","clone":"git clone https://github.com/KalinNonchev/gnomAD_DB.git","description":"Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.","language":"Python","stars":53,"topics":["database","genetics","rare-variant-analysis","gnomad","annotation","variant-analysis","bioinformatics","exome-sequencing","genomics","population-genetics"],"license":"MIT","category":"databases-storage","readme_excerpt":"gnomAD DB Changelog NEW version (April 2024) - release gnomAD WGS v4.1 and WES v4.1 - More information here. version (November 2023) - release gnomAD WGS v4.0 and WES v4.0 - gnomad version =[\"v2\" \"v3\" \"v4\"] argument has to be specified when initializing the database - minor fixes version (July 2022) - release gnomAD WGS v3.1.2 - minor bug fixes version (December 2021) - more available variant features present, check here - get maf from df renamed to get info from df - get maf from str renamed to get info from str - [DEPRECATED 11.2023] genome =[\"Grch37\" \"Grch38\"] argument has to be specified when initializing the database Why and What The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community. This package scales the huge gnomAD files (on average 120G/chrom) to a SQLite database with a size of <100G and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc. - here you can find all selected features given the genome version). (A query containing 300.000 variants takes 40s.) It extracts from a gnomAD vcf about 23 variant annotations. You can find further information about the exact fields here. The package works for all currently available gnomA","default_branch":null,"files":null,"tree":[],"storefront":"/r/KalinNonchev","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/KalinNonchev/gnomAD_DB/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}