Metadata-Version: 2.1
Name: array-as-vcf
Version: 1.0.1
Summary: Convert SNP array to VCF
Home-page: https://github.com/LUMC/array-as-vcf
Author: Sander Bollen, Redmar van den Berg
Author-email: KG_bioinf@lumc.nl
License: MIT
Description: # Array As VCF
        
        `array-as-vcf` is a small library and tool to 
        convert common SNP array formats to VCF format.
        
        There are four currently supported array formats:
        
        * Affymetrix (TSV export)
        * Cytoscan HD Array (TSV export)
        * Lumi 317k array (TSV export)
        * Lumi 370k array (TSV export)
        * Multi-sample OpenArray (TSV export)
        
        Binary formats are not (yet) supported.
         
        
        # Requirements
        
        * Python 3.6
        * requests
        
        # CLI usage
        
        The `array-as-vcf` tool will convert array files to VCF format.
        It will auto-detect the type of array file, and throw an error if it can't
        determine it. 
        
        The generated VCF file is printed to stdout.
        
        A sample name to be used in the VCF file _must_ be supplied.
        
        The REF and ALT alleles will be queried from Ensembl if no `lookup-table` is
        supplied. This requires a working internet connection, and can be quite slow
        due the amount of HTTP requests that are necessary.
        
        When supplied with `lookup-table`, no requests are made for the rsIDs 
        which exist within the lookup table. The lookup table is a JSON file,
        containing a single large object of shape:
        
        ```json
        {
          "rs0": "{ref_allele}:{alt_alleles}:{ref_is_minor_allele}"
        }
        ``` 
        
        E.g. 
        
        ```json
        {
          "rs1000003": "A:G:F"
        }
        ```
        
        If you have never run `array-as-vcf` before , you can run `array-as-vcf` sans lookup table
        and `dump` the generated internal lookup table to a file for next iterations.
        
        ```bash
        Usage: array-as-vcf [OPTIONS]
        
        Options:
          -p, --path PATH              Path to array file  [required]
          -b, --build [GRCh37|GRCh38]
          -s, --sample-name TEXT       Name of sample in VCF file
          -c, --chr-prefix TEXT        Optional prefix to chromosome names
          -l, --lookup-table PATH      Optional path to existing lookup table for
                                       rsIDs.
          -d, --dump PATH              Optional path to write generated lookup table
          --help                       Show this message and exit.
        
        ```
        
Keywords: array vcf SNP convert OpenArray Cytoscan lumi370k lumi317k Affymetrix
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
