7.1 convertVCF

Converting a VCF file to other formats

convertVCF converts a VCF file to a variety of file formats. Available output formats are:

• beagle
• geno
• LFMM
• posfile
• genfile

Detailed descriptions of the file formats are provided here.

7.1.1 Parameters

7.1.1.1 Input

--vcf Input_VCF_file.vcf.gz

Input VCF file.

7.1.1.2 Specific

--format format

Specify the format to be converted to. Options = beagle, geno, LFMM, posfile, genfile.

7.1.1.3 Engine

• General
• Population parameters
• Genome

7.1.2 Output

Any supported file format, see format options above.

7.1.3 Usage Example

# Simulate 5 samples in Hardy–Weinberg Equilibrium and write vcf file
atlas simulate --vcf --type HW --sampleSize 5

# Convert vcf file to beagle format
atlas convertVCF --vcf ATLAS_simulations.vcf.gz --format beagle