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 Input

Required inputs :

--vcf Input_vcf_file.vcf.gz VCF file with allelic depth field.

Optional inputs :

  • None

Specific Parameters :

--writeBED Write invariant sites to bed file.
--fixInt Fix integers that are printed as floats.
  • See Filter parameters to apply specific filters for bases, reads and parsing window setting.

Engine parameters that are common to all tasks can be found here.

7.4.2 Output

*.txt Text file with ratio of reference to the alternate allele.

7.4.3 Usage Example

#! /bin/bash

# Set atlas path
atlas=$(dirname "$0")/../build/atlas

# 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