genotype

apriha/lineage

tools for genetic genealogy and the analysis of consumer DNA test results

brentp/peddy

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

zhanxw/rvtests

Rare variant test software for next generation sequencing data

hall-lab/svtyper

Bayesian genotyper for structural variants

caleblareau/mgatk

mgatk: mitochondrial genome analysis toolkit

ArnovanHilten/GenNet

Framework for Interpretable Neural Networks

limix/pandas-plink

PLINK reader for Python.

sbslee/pypgx

A Python package for pharmacogenomics (PGx) research

dantaki/SV2

Support Vector Structural Variation Genotyper

0xTCG/aldy

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

mehrdadbakhtiari/adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

zheminzhou/EToKi

all methods related to Enterobase

MichaelSebero/Genetic-Trait-Detector

This python script detects known traits in raw human genetic data.

solgenomics/SNPbinner

SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.

selfdecode/rd-imputation-accuracy

Phasing and genotype Imputation comparison. Have been evaluated: BEAGLE 5.4, EAGLE 2.4.1, SHAPEIT 4, MINIMAC 4, IMPUTE 5, using accuracy metrics like: IQS(Imputation Quality score), r2 (Pearson correlation), Concordance.

dvitale199/GenoTools

GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for computational biology and genetics research.

teepean/BAM-Analysis-Kit

shz9/magenpy

Modeling and Analysis of (Statistical) Genetics data in python

YaoLab-Bioinfo/ECOGEMS

Efficient compression and retrieve of genotype data with integer sparse matrices

cfe-lab/MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C

lifeomic/spark-vcf

Spark VCF data source implementation for Dataframes

Gregor-Mendel-Institute/SNPmatch

A simple python library to identify the most likely strain from the population

lauzingaretti/pSBVB

Manual

galantelab/sideRETRO

A pipeline for detecting Somatic Insertion of DE novo RETROcopies

Endika/genome_report

Your genome report

AmirHoseinSafari/Genotype-collector-and-SNP-dataset-creator

Collecting Genotypes from ENA and make their SNPs

p4rkerw/SALSA

Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts

akiomiyao/ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

cnettel/cnF2freq

Compute haplotype and genotype probabilities, and perform imputation, in arbitrary pedigrees, including cases under possible observational errors.

dr-roshyara/fcgene

Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST.

UofS-Pulse-Binfo/nd_genotypes

Drupal/Tripal: Tripal interface for Chado Natural Diversity Genotypic data.

ariadnacilleros/Cis-mQTL-mapping-protocol-for-methylome

juliedwhite/GenotypeProcessing

Pipeline with lots of user input for processing SNP data towards ADMIXTURE and/or imputation

shz9/tokyo-symposium-2024

Tokyo Symposium on Genomic Medicine (2024)

Zhangliubin/GBC

GBC (short for GenoType Blocking Compressor) is a blocking compressor for genotype data, which aims at creating a unified and flexible structure-GenoType Block (GTB) for genotype data in the variant call format (VCF) files.