![]() Pass with no need for intermediate temporary files. ![]() In the single file case, the input VCF is converted to the output Zarr file in a single sequential Processing multiple inputs is more work than a single file, since behind the scenes each input isĬonverted to a separate temporary Zarr file on disk, then these files are concatenated and rechunked > from sgkit.io.vcf import vcf_to_zarr > vcf_to_zarr (, "output.zarr" ) If there are multiple files, then pass a list: The sgkit.io.vcf.vcf_to_zarr() function can accept multiple files, and furthermore, each of theseįiles can be partitioned to enable parallel processing. ![]() load_dataset ( "output.zarr" ) > ds Dimensions: (alleles: 4, ploidy: 2, samples: 1, variants: 19910) Dimensions without coordinates: alleles, ploidy, samples, variants Data variables: call_genotype (variants, samples, ploidy) int8 dask.array call_genotype_mask (variants, samples, ploidy) bool dask.array call_genotype_phased (variants, samples) bool dask.array sample_id (samples) variant_allele (variants, alleles) object dask.array variant_contig (variants) int8 dask.array variant_id (variants) object dask.array variant_id_mask (variants) bool dask.array variant_position (variants) int32 dask.array Attributes: contigs: max_variant_allele_length: 48 max_variant_id_length: 1 > import sgkit as sg > from sgkit.io.vcf import vcf_to_zarr > vcf_to_zarr ( "CEUTrio.20.21.gatk3.4.g.vcf.bgz", "output.zarr" ) > ds = sg. To install sgkit with VCF support using pip (there is no conda package): VCF support is an “extra” feature within sgkit and requires additional Support for polyploid and mixed-ploidy genotypes. Input and output files can reside on local filesystems, Amazon S3, or Index, and each region is processed in parallel using Dask.Ĭontrol over Zarr chunk sizes allows VCFs with a large number of samples ![]() Large VCF files can be partitioned into regions using a Tabix (. Reads bgzip-compressed VCF and BCF files. The sgkit.io.vcf.vcf_to_zarr() function converts one or more VCF files to Zarr files stored in ![]() Example: converting 1000 genomes VCF to Zarr ![]()
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