snp_conversion

• FILE: SNP_conversion.py
• AUTH: Emily Herman (eherman@ualberta.ca)
• DATE: APR 7, 2020
• VERS: 3.0

Please see the snp_conversion wiki for more information about the program.

General Description

snp_conversion is a collection of tools for working with genotype data from Illumina and Affymetrix SNP panels. The program can:

• Check that all SNPs in the panel are consistently formatted
• Determine the format of a panel
• Convert a consistently formatted panel to a different format
• Merge panels of the same format
• Create PLINK flat files from SNP panel genotype data
• Assess concordance of genotype data in the panel file with that of a user-specified VCF file
• Generate a VCF file from a SNP panel file

Usage information

usage: snp_conversion [-h] Tools ...

A selection of tools for working with genotype data from Illumina and
Affymetrix SNP panels To see the full usage for each Utility: ./snp_convserion
[Utility] --help

positional arguments:
  Tools
    check_format        Checks the format of the input file(s)
    convert_file        Converts input file(s) to user-specified format
    merge_files         Merges files of the same format
    conversion_list     Lists all species and assembly names available
    genotype_concordance
                        Determines concordance between SNP panel genotypes and
                        VCF file genotypes
    vcf_generator       Converts SNP panel file to VCF format file

There are five main tools within snp_conversion:

1. check_format
2. convert_file
3. merge_files
4. genotype_concordance
5. vcf_generator

See Install page and Quick Start Guide to get started using the snp_conversion tools with a test dataset.

Most snp_conversion tools rely on genotype conversion files to check input data formatting. See the Genotype Conversion Files section for information about generating these files.