mip-poolfreq

Tools to estimate allele frequencies and genotype frequencies from pooled sequencing data generated with Molecular Inversion Probes (MIPs).

This repository contains two complementary command-line tools:

• Afreq – extract reference allele frequencies and read depths from VCF files

• Gfreq – estimate genotype frequencies in pooled samples using allele frequencies and sequencing depth information

The typical analysis workflow is illustrated below.

VCF with AD field
      │
      ▼
Afreq estimate
      │
      ├── ref allele frequencies
      └── total depths
              │
              ▼
        Gfreq estimate
              │
              ▼
   genotype frequency estimates

Both tools are distributed together in a single container.

Container image

A pre-built OCI image is available on GitHub Container Registry:

ghcr.io/ge2pop/mip-poolfreq

It can be pulled with Apptainer to obtain a local .sif image:

apptainer pull mip-poolfreq.sif docker://ghcr.io/ge2pop/mip-poolfreq:latest

Show available commands:

apptainer exec mip-poolfreq.sif --help

Tools

Afreq

Compute reference allele frequencies and total read depths from the AD field of a VCF file.

Typical use case: transform raw variant calls into allele frequency matrices that can be used as input for downstream analyses.

Documentation: Afreq/README.md

Gfreq

Estimate genotype frequencies in pooled samples from allele frequencies and sequencing depth data produced by Afreq.

Includes several commands:

• estimate – estimate genotype frequencies

• eval – evaluate estimation accuracy in controlled mixtures with known composition

• maf – compute minor allele frequencies

• depth – summarize sequencing depth per marker

Documentation: Gfreq/README.md

Citation

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License

MIT License