DESCRIPTION: PLINK: a tool set for whole-genome association and population-based linkage analyses. This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab, and others.
URL : https://www.cog-genomics.org/plink/1.9/
CITATION: Purcell, Shaun, et al. "PLINK: a tool set for whole-genome association and population-based linkage analyses." The American journal of human genetics 81.3 (2007): 559-575.
PLINK2
SHORT NAME: PLINK2
FULL NAME: PLINK2
YEAR: 2015
DESCRIPTION: The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.
URL : https://www.cog-genomics.org/plink/2.0/
CITATION: Chang, Christopher C., et al. "Second-generation PLINK: rising to the challenge of larger and richer datasets." Gigascience 4.1 (2015): s13742-015.
KEY WORDS:
QCTOOL v2
SHORT NAME: QCTOOL
FULL NAME: QCTOOL
DESCRIPTION: QCTOOL is a command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data.
DESCRIPTION: Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data.
URL : https://hail.is/
CITATION: Hail Team. Hail 0.2.13-81ab564db2b4. https://github.com/hail-is/hail/releases/tag/0.2.13.
LDSC - ld score calculation
SHORT NAME:LDSC
FULL NAME:LD Score Regression
YEAR:2015
DESCRIPTION:ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
URL:https://github.com/bulik/ldsc
CITATION :Bulik-Sullivan, Brendan K., et al. "LD Score regression distinguishes confounding from polygenicity in genome-wide association studies." Nature genetics 47.3 (2015): 291-295.
GCTA - ld matrix
SHORT NAME: GCTA
FULL NAME:Genome-wide complex trait analysis (GCTA)
YEAR:2010
DESCRIPTION:GCTA-GREML analysis:GCTA can simulate a GWAS based on real genotype data.
DESCRIPTION: LDstore is a computationally efficient program for estimating and storing Linkage Disequilibrium (SNP correlations). It combines some of the best features from RAREMETALWORKER and PLINK by implementing parallel processing using OPENMP and storing of the SNP correlations with information about the SNPs in the same binary file for fast lookups. LDstore is therefore the ideal tool for sharing SNP correlations in large-scale meta-analyses of genome-wide association studies and for on-the-fly computing/querying within web portals.
URL : http://www.christianbenner.com/#
CITATION: Benner, C. et al. Prospects of fine-papping trait-associated genomic regions by using summary statistics from genome-wide association studies. Am. J. Hum. Genet. (2017).
MungeSumstats
SHORT NAME: MungeSumstats
FULL NAME: MungeSumstats
YEAR: 2021
DESCRIPTION: a Bioconductor package for the standardization and quality control of many GWAS summary statistics
CITATION: Murphy, Alan E., Brian M. Schilder, and Nathan G. Skene. "MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics." Bioinformatics 37.23 (2021): 4593-4596.
gwaslab
SHORT NAME: gwaslab
FULL NAME: gwaslab
YEAR: 2022
DESCRIPTION: a python package for handling GWAS sumstats.