↪️Converting VCF to BED files

Convert

1. Choose VCF: Click to upload a Variant Call Format (VCF) file, which contains genetic variation data.

2. Choose variants (optional): Optionally upload a file with specific genetic variants to be included in the conversion process.

3. MAF input box: Set the minor allele frequency (MAF) threshold for filtering variants. Variants with a MAF below this value will be excluded.

4. Missing genotype rate input box: Enter the maximum allowable rate of missing genotypes per variant. Variants with missing data above this rate will be excluded.

5. Convert button: Start the conversion of the VCF file to the BED/BIM/FAM file format, applying the specified MAF and missing genotype filters.

Supported file formats

VCF file format (including vcf.gz) and PLINK BED/BIM/FAM format are supported for all GWAS methods. The VCF files must converted to BED/BIM/FAM file format.

https://github.com/snowformatics/data/blob/cd8ac371fe669711430a6a4d7c00960082b3cd4b/gwastic_test_data/example.vcf.gz

VCF example file