seqdata.read_vcf

seqdata.read_vcf(name, out, vcf, fasta, samples, bed, batch_size, fixed_length, n_threads=1, samples_per_chunk=10, alphabet=None, max_jitter=0, overwrite=False, splice=False)

Read a VCF file and return a Dataset.

Parameters:

  • name (str) – Name of the sequence variable in the output dataset.

  • out (PathType) – Path to the output Zarr store where the data will be saved. Usually something like /path/to/dataset_name.zarr.

  • vcf (PathType) – Path to the VCF file.

  • fasta (PathType) – Path to the reference genome.

  • samples (List[str]) – List of sample names to include.

  • bed (Union[PathType, pd.DataFrame]) – Path to a BED file or a DataFrame with columns “chrom”, “start”, and “end”.

  • batch_size (int) – Number of regions to read at once. Use as many as you can fit in memory.

  • fixed_length (Union[int, bool]) – Whether your sequences have a fixed length or not. If they do, the data will be stored in a 2D array as bytes, otherwise it will be stored as unicode strings.

  • n_threads (int) – Number of threads to use for reading the VCF file.

  • samples_per_chunk (int) – Number of samples to read at a time.

  • alphabet (Optional[Union[str, sp.NucleotideAlphabet]]) – Alphabet the sequences have.

  • max_jitter (int) – Maximum jitter to use for sampling regions.

  • overwrite (bool) – Whether to overwrite an existing dataset.

  • splice (bool) – TODO

Returns:

xarray dataset

Return type:

xr.Dataset