https://github.com/maehler/vcfsubsample

Subsample a VCF file in order to fix the minor allele frequency across SNPs
https://github.com/maehler/vcfsubsample

bioinformatics genomics genotype vcf

Last synced: 7 months ago
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Subsample a VCF file in order to fix the minor allele frequency across SNPs

• Host: GitHub
• URL: https://github.com/maehler/vcfsubsample
• Owner: maehler
• License: mit
• Created: 2017-03-09T15:41:57.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2020-06-11T09:12:32.000Z (over 5 years ago)
• Last Synced: 2025-01-30T19:47:58.572Z (8 months ago)
• Topics: bioinformatics, genomics, genotype, vcf
• Language: C
• Size: 20.5 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Subsample genotype data

In genome wide association (GWA) studies a recurring problem is differences in statistical power due to sample sizes and rare sequence variants. One way to account for this is to subsample the data in order to "lock" the minor allele frequency (MAF) in the data set, *i.e.* all SNPs will have the same MAF.

This is a tool that will help with this subsampling.

## Requirements

- CMake

- htslib

- argp

On Mac, argp can can be installed through Homebrew with the argp-standalone formula.

## Build

```bash

git clone --recursive https://github.com/maehler/vcfsubsample

cd vcfsubsample

mkdir build

cd build

cmake ..

make

make install

```

## Usage

```

> vcfsubsample --help

Usage: vcfsubsample [OPTION...] VCF

vcfsubsample -- subsample a VCF file in order to fix the minor allele frequency

across SNPs

     --exact-samples        Subsample to exactly --min-samples

     --keep-missing         Keep SNPs for which subsampling is not possible

     --maf=FLOAT            Target MAF to aim for

     --margin=FLOAT         Allow target MAF within this margin

     --max-mgf=FLOAT        Maximum genotype frequency to allow for each SNP

     --min-samples=N        Minimum number of samples to allow

     --samplenames          Output names of suggested samples to use for

                            subsampling instead of the number of genotypes of

                            each class

 -?, --help                 Give this help list

     --usage                Give a short usage message

 -V, --version              Print program version

Report bugs to .

```

Genotype data can be read from stdin by using `-` for the VCF filename.