GlfSingle

glfSingle is a GLF-based variant caller for next-generation sequencing data. It takes a GLF format genotype likelihood file as input and generates a VCF-format set of variant calls as output.

Basic Usage Example

Here is an example of how glfSingle works:

  glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log

Command Line Options

 -g genotype likelihood file    Specifies the name of the input GLF-format genotype likelihood file
 -b base call file              Specifies the name of the output VCF-format base call file
 -s sample label                Specifies a label for the sample being analyzed, which will be included in the output VCF file
 -p threshold                   The threshold for base calling. Base calls will be made when their posterior likelihood exceeds threshold

 --minMapQuality threshold      Positions where the root-means squared mapping quality falls below this threshold will be excluded.
 --minDepth      threshold      Positions where the read depth falls below this threshold will be excluded.
 --maxDepth      threshold      Positions where the read depth exceeds this threshold will be excluded.
 --reference                        Positions called as homozygous reference will be included in the output.  

TODO

Support for X chromosome variant calling.

Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.