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Jump to navigationJump to searchCreated page with ''''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 [[VC…'
'''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 <code>glfMultiples</code> works:
glfTrio --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.
=== X Chromosome Variant Calling ===
--xChr ''chromosomeName'' Label for the 'X' chromosome in the GLF file
--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)
== Model for Variant Calling ==
== 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.
== 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 <code>glfMultiples</code> works:
glfTrio --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.
=== X Chromosome Variant Calling ===
--xChr ''chromosomeName'' Label for the 'X' chromosome in the GLF file
--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)
== Model for Variant Calling ==
== 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.
