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README_16_store_allele_data_vcf.md

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Store allele data (from NPY to VCF)

The MergeGenome store-vcf command reads from a provided NPY file with a two-dimensional matrix containing splitted maternal and paternal strands and stores this data in the three-dimensional calldata/GT field of the provided VCF file. Additionaly, --binary-indexes flag allows removing all incorrect SNPs with a 0 in the the NPY file with the binary indexes. Therefore, the MergeGenome store-vcf command can be used to integrate the output of other preprocessing softwares back into a VCF file.

Usage

$ python3 MergeGenome.py store-vcf -q <query_vcf_file> --n <query_npy_file> o <output_folder>

Input flags include:

  • -q, --vcf-query Path, Path to query .vcf file (required).
  • -n, --npy-query Path, Path to query .npy file (required).
  • -o, --output-folder PATH, Path to output folder (required). Note: make sure a '/' appears at the end of the output folder.
  • -b, --binary-indexes PATH, Path to binary indexes, where 1 means the SNP is correct and 0 that it is to be removed (optional).
  • -d, --debug PATH, Path to file to store info/debug messages (optional).

Output

  • A .vcf file with calldata/GT from the provided .npy file and, optionally, remove undesired SNPs. The new file will receive the same base name as the input .vcf file, but ending with '_from_npy.vcf'.
  • If --debug, a .log or .txt file with information regarding the dimensions of the data (number of samples and number of SNPs).

Examples

  1. Store allele data in .npy format by splitting the maternal and paternal strands:
$ python3 MergeGenome.py store-allele -q query.vcf -o ./output/ -s separated -f .npy
  1. Store allele data in .h5 format by averaging the maternal and paternal strands:
$ python3 MergeGenome.py store-allele -q query.vcf -o ./output/ -s averaged -f .h5