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 example1.vcf.gz

VCF file with allelic depth field.

Optional inputs :

• None

Specific Parameters :

• None

• 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 --logFile simulate.out

# Diagnose vcf file
$atlas VCFDiagnostics --vcf ATLAS_simulations.vcf.gz --logFile VCFDiagnostics.out