Difference between revisions of "GlfSingle"
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== Model for Variant Calling == | == Model for Variant Calling == | ||
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+ | == Download == | ||
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+ | For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website]. | ||
== TODO == | == TODO == |
Revision as of 13:01, 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
Download
For the current of glfSingle, please go to our GLF Tools Website.
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.