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.
- CMake
- htslib
- argp
On Mac, argp can can be installed through Homebrew with the argp-standalone formula.
git clone --recursive https://github.com/maehler/vcfsubsample
cd vcfsubsample
mkdir build
cd build
cmake ..
make
make install> 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 <[email protected]>.
Genotype data can be read from stdin by using - for the VCF filename.