67 Open source projects that are alternatives of or similar to vcf2gwas

Haplotype VCF comparison tools

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Visual Machine Learning of Genome-Phenome Associations

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

Efficient variant-call data storage and retrieval library using the TileDB storage library.

calcardbackup: moved to https://codeberg.org/BernieO/calcardbackup

A Java API for high-throughput sequencing data (HTS) formats.

Cancer Predisposition Sequencing Reporter (CPSR)

Bayesian genotyper for structural variants

A fluent builder class for vCard files.

A DNA Sequence Alignment/Map (SAM) library for Clojure

C library for high-throughput sequencing data formats

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

GWAS summary statistics files QC tool

Perform GWAS using the FarmCPU model.

cython + htslib == fast VCF and BCF processing

Mixed models @lme4 + custom covariances + parameter constraints

Personal Cancer Genome Reporter (PCGR)

Annotation of VCF variants with functional impact and from databases (executable+library)

Graph realignment tools for structural variants

simple viewer for variant call format using htslib

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

find large indels (in the blind spot between GATK/freebayes and SV callers)

highly-efficient & lightweight mutation signature matrix aggregation

vembrane filters VCF records using python expressions

Syntax highlighting for computational biology

This vCard PHP library can easily parse or generate/export vCards as .vcf

Spark VCF data source implementation for Dataframes

📊 Identify cell types and pathways affected by genetic risk loci.

Frequently used commands in bioinformatics

Find causal cell-types underlying complex trait genetics

convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

A faster lmm for GWAS. Supports GPU backend.

✂️ ⚡️ Rapid haploid variant calling and core genome alignment

Learning the Variant Call Format

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Toolset for SV simulation, comparison and filtering

📊Evaluating, filtering, comparing, and visualising VCF

Syntax highlighting for computational biology

Heritability, genetic correlation and functional enrichment estimation for case-control studies

A collection of scripts and notes related to genomics and bioinformatics

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

Structural variant toolkit for VCFs

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

vCard Serializer and Parser for C#

Quantitative Trait Cluster Association Test in R

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

A standalone and free application to explore genetics variations from VCF file

Generic germline variant annotation pipeline

Rare variant test software for next generation sequencing data

Scalable genomic data analysis.

tools for reading, writing, merging, and remapping SNPs

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

Method to optimally select samples for validation and resequencing

Adjacency-constrained hierarchical clustering of a similarity matrix

Genomic VCF to tab-separated values

Powerful statistics for VCF files

🔧 Simple script in python to convert CSV files to VCF