Pinned Repositories
bedtools2
bedtools - the swiss army knife for genome arithmetic
bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
DosageConvertor
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.
Eagle
Haplotype phasing software
GEMMA
Genome-wide Efficient Mixed Model Association
Genotype_Imputation_Pipeline
Final version of the pipeline for processing TOPMED and other dbGaP datasets, includes: automatic identification of reference genome build and selection of correct chain file, mapping to GRCh37 reference build, initial quality control, ancestry analysis, post-ancestry quality control, phasing, imputation, post-imputation quality control.
imputation_accuracy_calculator
ldsc
LD Score Regression (LDSC)
Minimac3
Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
Minimac4
scau-drr's Repositories
scau-drr/bedtools2
bedtools - the swiss army knife for genome arithmetic
scau-drr/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
scau-drr/DosageConvertor
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.
scau-drr/Eagle
Haplotype phasing software
scau-drr/GEMMA
Genome-wide Efficient Mixed Model Association
scau-drr/Genotype_Imputation_Pipeline
Final version of the pipeline for processing TOPMED and other dbGaP datasets, includes: automatic identification of reference genome build and selection of correct chain file, mapping to GRCh37 reference build, initial quality control, ancestry analysis, post-ancestry quality control, phasing, imputation, post-imputation quality control.
scau-drr/imputation_accuracy_calculator
scau-drr/ldsc
LD Score Regression (LDSC)
scau-drr/Minimac3
Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
scau-drr/Minimac4
scau-drr/mtag
Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
scau-drr/patchwork
The Composer of ggplots
scau-drr/vcftools
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.