Difference between revisions of "GlfMultiples"
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--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. | ||
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=== X Chromosome Variant Calling === | === X Chromosome Variant Calling === | ||
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--xStart ''sexChromosomeStart'' Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36) | --xStart ''sexChromosomeStart'' Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36) | ||
--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36) | --xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36) | ||
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== Download == | == Download == | ||
Revision as of 05:38, 20 May 2010
glfMultiples is a GLF-based variant caller for next-generation sequencing data. It takes a set of GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output.
Basic Usage Example
In a typical command line, a series of options controlling variant calling appear first and are followed by a trailing list of GLF-format likelihood files. Here is an example of how glfMultiples works:
glfMultiples --minMapQuality 30 --minTotalDepth 60 --maxTotalDepth 240 -b YRI.SLX.vcf YRI/NA*.SLX.glf > YRI.SLX.log
Command Line Options
Basic Output Options
-b baseCallFile Specifies the name of the output VCF-format base call file -p threshold The threshold for base calling. Base calls will be made when their posterior likelihood exceeds threshold
Filtering According to Depth and Map Quality
--minMapQuality threshold Positions where the root-means squared mapping quality falls below this threshold will be excluded.
--strict When the map quality is interpreted strictly, all three trio individuals must exceed minMapQuality
before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.
--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.
Download
The current version is available for download from here.
TODO
Support for X chromosome variant calling.
Support for two-pass depth filter that looks at the data to work out appropriate thresholds for shallow and deep coverage.
