Difference between revisions of "GlfSingle"
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--minDepth ''threshold'' Positions where the read depth 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. | --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded. | ||
− | --reference | + | --reference Positions called as homozygous reference will be included in the output. |
− | + | ||
== Model for Variant Calling == | == Model for Variant Calling == | ||
Revision as of 12:24, 24 March 2010
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.
Model for Variant Calling
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.