7.4 VCFDiagnostics

Diagnosing a VCF file

VCFDiagnostics estimates the fraction of reference to the alternate allele. This task requires the input VCF file to have allelic depth field. None of the VCF files generated by any of the ATLAS tasks have allelic depth field.

7.4.1 Parameters

7.4.1.1 Input

--vcf Input_vcf_file.vcf.gz

VCF file with allelic depth field.

7.4.1.2 Specific Parameters

--writeBED	Write invariant sites to bed file
--fixInt	Fix integers that are printed as floats

7.4.1.3 Engine

• General
• Population parameters
• Genome

7.4.2 Output

*.txt

Text file with ratio of reference to the alternate allele

7.4.3 Usage Example

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

# Diagnose vcf file
atlas VCFDiagnostics --vcf ATLAS_simulations.vcf.gz