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[[Category:Software]]
'''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.
'''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.
== 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.
To learn about default values for these options, simply run the program with no arguments.
== Model for Variant Calling ==
== Model for Variant Calling ==
glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''.
Ingredients that go into prior:
*All sites have an equal probability of showing polymorphism:
**P(non-reference base) = 0.001
*When a site shows polymorphism, it is usually heterozygous:
**P(non-reference heterozygote) = 0.01 * 2/3
**P(non-reference homozygote) = 0.01 * 1/3
*Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants
**transition has 2/3 probability
**each transversion has 1/6 probability
*'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio
**updated by Yancy Lo, 9/24/2012
**each mutation has a 1/3 probability
**add --uniformTsTv in command line to enable this alternative mutation model
**download glfSingle with this new implementation here: [[File:Generic-glfSingle-2013-09-25.tar.gz]]
== Download ==
For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ 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.
