Difference between revisions of "GlfSingle"
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== Command Line Options == | == 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 == | == Model for Variant Calling == |
Revision as of 18:13, 14 November 2009
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.