GlfSingle - Revision history

Yancylo: /* Model for Variant Calling */

2013-09-26T15:34:41Z

Model for Variant Calling

← Older revision		Revision as of 11:34, 26 September 2013
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	**each mutation has a 1/3 probability		**each mutation has a 1/3 probability
	**add --uniformTsTv in command line to enable this alternative mutation model		**add --uniformTsTv in command line to enable this alternative mutation model
	**download [[File:Generic-glfSingle-2013-09-25.tar.gz]]		**download glfSingle with this new implementation here: [[File:Generic-glfSingle-2013-09-25.tar.gz]]

	== Download ==		== Download ==

2013-09-26T15:34:16Z

Model for Variant Calling

← Older revision		Revision as of 11:34, 26 September 2013
Line 39:		Line 39:
	**each mutation has a 1/3 probability		**each mutation has a 1/3 probability
	**add --uniformTsTv in command line to enable this alternative mutation model		**add --uniformTsTv in command line to enable this alternative mutation model
	**download [[~~here~~ ]]		**download [[File:Generic-glfSingle-2013-09-25.tar.gz]]

	== Download ==		== Download ==

2013-09-25T20:16:11Z

Model for Variant Calling

← Older revision		Revision as of 16:16, 25 September 2013
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	*'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio		*'''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		**each mutation has a 1/3 probability
	**add --uniformTsTv in command line to enable this alternative mutation model		**add --uniformTsTv in command line to enable this alternative mutation model
	**download [here ]		**download [[here ]]

	== Download ==		== Download ==

2013-09-25T20:15:39Z

Model for Variant Calling

← Older revision		Revision as of 16:15, 25 September 2013
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	**each transversion has 1/6 probability		**each transversion has 1/6 probability

	*New implementation: Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio		*'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio
	**each mutation has a 1/3 probability		**each mutation has a 1/3 probability
	**add --uniformTsTv in command line to enable this alternative mutation model		**add --uniformTsTv in command line to enable this alternative mutation model
	**download here		**download [here ]

	== Download ==		== Download ==

2013-09-25T20:14:26Z

Command Line Options

← Older revision		Revision as of 16:14, 25 September 2013
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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.
	--reference Positions called as homozygous reference will be included in the output.		--reference Positions called as homozygous reference will be included in the output.
	~~--uniformTsTv Use a uniform prior for transition-to-transversion ratio.~~

	To learn about default values for these options, simply run the program with no arguments.		To learn about default values for these options, simply run the program with no arguments.

2013-09-25T20:14:09Z

Model for Variant Calling

← Older revision		Revision as of 16:14, 25 September 2013
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	*P(non-reference heterozygote) = 0.01 2/3		*P(non-reference heterozygote) = 0.01 2/3
	*P(non-reference homozygote) = 0.01 1/3		*P(non-reference homozygote) = 0.01 1/3
	*~~Two options of mutation~~ model:		*Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants
	**Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants		**transition has 2/3 probability
	***transition has 2/3 probability		**each transversion has 1/6 probability
	***each transversion has 1/6 probability
	**Uniform (uninformative) prior for transition to transversion ratio		*New implementation: Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio
	***each mutation has a 1/3 probability		**each mutation has a 1/3 probability
			**add --uniformTsTv in command line to enable this alternative mutation model
			**download here

	== Download ==		== Download ==

2013-09-23T19:32:14Z

Model for Variant Calling

← Older revision		Revision as of 15:32, 23 September 2013
Line 34:		Line 34:
	*Two options of mutation model:		*Two options of mutation model:
	**Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants		**Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants
	**Uniform prior for transition to transversion ratio ~~(1:~~1)		***transition has 2/3 probability
			***each transversion has 1/6 probability
			**Uniform (uninformative) prior for transition to transversion ratio
			***each mutation has a 1/3 probability

	== Download ==		== Download ==

2013-09-23T19:23:51Z

Command Line Options

← Older revision		Revision as of 15:23, 23 September 2013
Line 19:		Line 19:
	--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.
	--reference Positions called as homozygous reference will be included in the output.		--reference Positions called as homozygous reference will be included in the output.
	--~~uTsTv~~ Use a uniform prior for transition-to-transversion ratio.		--uniformTsTv Use a uniform prior for transition-to-transversion ratio.

	To learn about default values for these options, simply run the program with no arguments.		To learn about default values for these options, simply run the program with no arguments.

2013-09-23T19:19:23Z

Command Line Options

← Older revision		Revision as of 15:19, 23 September 2013
Line 19:		Line 19:
	--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.
	--reference Positions called as homozygous reference will be included in the output.		--reference Positions called as homozygous reference will be included in the output.
			--uTsTv Use a uniform prior for transition-to-transversion ratio.

	To learn about default values for these options, simply run the program with no arguments.		To learn about default values for these options, simply run the program with no arguments.

2013-09-23T19:17:41Z

Model for Variant Calling

← Older revision		Revision as of 15:17, 23 September 2013
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	== 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
			*Two options of mutation model:
			**Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants
			**Uniform prior for transition to transversion ratio (1:1)

	== Download ==		== Download ==