Overview

Input

• a VCF file

Output

• a .txt file

Usage Example

.. sourcecode:: bash

./atlas task=VCFToBeagle vcf=example.vcf.gz minDepth=2 minNumSamplesWithData=200 minVariantQuality=40 keepChromosomes=chr1,chr2,chr17

Specific Arguments

• vcf: VCF file (gzipped).
• limitLines: amount of lines to be read from VCF file.
• minDepth: minimal depth per site.
• minNumSamplesWithData: at least this many samples need to have data in order to keep a locus.
• minVariantQuality: minimal variant quality in order to be keep a locus.
• keepChromosomes: only loci on these chromosomes are kept. The argument can be a filename (which needs to end with .txt); or a comma-seperated list of chromosome names.
• reportFreq: after how many parsed loci to report progress.

Engine Parameters

Engine parameters that are common to all tasks can be found here <https://bitbucket.org/WegmannLab/atlas/wiki/Engine%20Parameters>_.