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A tiny tool for recoding alleles in a VCF.

This aims to be an easy way to recode alleles from major/minor to ancestral/derived. You only need:

  • A .vcf(.gz) (Phased, or unphased, but you must specify this).
  • A .fasta(.gz) with ancestral states of each base.

Usage is pretty straightforward:

aavcf   -v your.vcf(.gz) \
        -f your.fasta(.gz) \
        -l your.log \

I've also provided vcf, vcf_line, and fasta classes in fasta.cpp/.h for extensibility. Each of these have a read,write, and get_allele (either for a particular entry or position) methods and are just abstractions of std::vector and std::string read in directly from data.

Installation

Short version: Same as any project build on CMake.

Slightly longer version:

mkdir build; cd build; cmake
make

Creating an empty build directory allows you to easily delete all the CMake build instructions if you so desire without a fresh clone.

Usage Flags

  • -v / --vcf: The path to a .vcf(.gz) file in 4.1-4.3 file format.
    • Currently only one sample VCFs are acceptable input.
  • -f / --fasta: The path to a .fasta(.gz) file on the same build as the VCF (i.e. the genomic coordinates are the same).
  • -l / --log: Path to a log file to store all information on actions taken.
    • Defaults to ./log.txt.
  • -h / --help: Will unsurprisingly show you the help menu.

Actions

aavcf will do one of four things for each variant in the VCF:

  1. Do nothing: If the ancestral allele is already the reference, no action is taken.
  2. Flip alleles (Flip in log): If the ancestral is the alternate, the coding is flipped.
  3. Uninformative allele (UnInfo in log): The ancestral allele is unknown, so derived state cannot be found. Code all alleles to 0.
  4. Different alleles (DifAlt in log): The ancestral allele is neither the reference nor the alternative, so no information is known. Code all alleles to 0.

C++ Class usage

To construct a fasta:

fasta new (std::string path_to_fasta);
  • new.get_allele(unsigned int pos) will retrieve an allele at a position.

To construct a vcf

vcf new (std::string path_to_vcf, char delim = '\t')
  • new.entries is a std::vector<vcf_line>, so the nth variant is retrieved with new.entries[i].
  • Each entry in the VCF for each variant is mutable and can be accessed by its standard name: new.entries[i].id = "rs1".
  • To write the VCF out, including meta data, simply call the new.write(std::string path) method.