SNP - Revision history

Raj at 03:24, 2 June 2016

2016-06-02T03:24:31Z

← Older revision		Revision as of 03:24, 2 June 2016
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			[[Category:Readings]] [[Category:Rajkumar]] [[Category:Biology]]

	=Base Calling=		=Base Calling=

2016-05-23T04:02:50Z

← Older revision		Revision as of 04:02, 23 May 2016
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	** HapMap data (Go-through, how haplotypic frequency will help in filtering the best SNPs )		** HapMap data (Go-through, how haplotypic frequency will help in filtering the best SNPs )
	** Deviations from HWE (Estimate the allelic frequencies when HD is estimated and figure out how to estimate the variant SNPs to filter them off)		** Deviations from HWE (Estimate the allelic frequencies when HD is estimated and figure out how to estimate the variant SNPs to filter them off)

			----
			[http://link.springer.com/article/10.1007/s11032-016-0476-9 Pooled_Mapping]

2016-05-17T09:43:51Z

← Older revision		Revision as of 09:43, 17 May 2016
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	** Phred score of ''Q'' should be = 10 to the power ''Q'' by 10 or less. This is done by alignning with the reference with the known SNPs		** Phred score of ''Q'' should be = 10 to the power ''Q'' by 10 or less. This is done by alignning with the reference with the known SNPs

	= ~~'''~~Homo and Heterozgous SNPs in a diploid~~'''~~=		= Homo and Heterozgous SNPs in a diploid=
	* Homozygous -> If an SNP (different than ref) base is counted across the read depth to be more than 80%		* Homozygous -> If an SNP (different than ref) base is counted across the read depth to be more than 80%
	* Hetorozygous -> If an SNP (different than ref) base is counted across the read depth to be less than 80%		* Hetorozygous -> If an SNP (different than ref) base is counted across the read depth to be less than 80%

2016-05-17T09:43:32Z

@@ Line 1: / Line 1: @@
-=SNP Filtering Plans=
-==Base Calling==
+=Base Calling=
 * Minimum Read depth
 * Based on Phred scores
@@ Line 8: / Line 8: @@
 ** Essential
 ** Phred score of ''Q'' should be = 10 to the power ''Q'' by 10 or less. This is done by alignning with the reference with the known SNPs
 =Plan for SNP calling=
 * Assumptions

2016-05-17T09:36:13Z

Plan for SNP calling

← Older revision		Revision as of 09:36, 17 May 2016
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	** Cross check the SNPs against all the 18 genotypes vs contrasting types		** Cross check the SNPs against all the 18 genotypes vs contrasting types
	* Filtering		* Filtering
	**		** Use of LD (Software would estimate this)
			** HapMap data (Go-through, how haplotypic frequency will help in filtering the best SNPs )
			** Deviations from HWE (Estimate the allelic frequencies when HD is estimated and figure out how to estimate the variant SNPs to filter them off)

2016-05-17T09:33:27Z

Plan for SNP calling

← Older revision		Revision as of 09:33, 17 May 2016
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	** LD based SNP calling		** LD based SNP calling
	** Cross check the SNPs against all the 18 genotypes vs contrasting types		** Cross check the SNPs against all the 18 genotypes vs contrasting types
			* Filtering
			**

2016-05-17T09:32:04Z

SNP Filtering Plans

← Older revision		Revision as of 09:32, 17 May 2016
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	*** Possible only when multi samples are used		*** Possible only when multi samples are used
	*** Software that uses LD for SNP calling is Beagle, IMPUTE2, QCall, MaCH		*** Software that uses LD for SNP calling is Beagle, IMPUTE2, QCall, MaCH


	=Plan for SNP calling=		=Plan for SNP calling=

2016-05-17T09:29:32Z

Base Calling

← Older revision		Revision as of 09:29, 17 May 2016
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	** This is true of the depth is minimum of 20x		** This is true of the depth is minimum of 20x
	* Accuracy in SNP calling		* Accuracy in SNP calling
	** Accuracy can be improved from single(Ref vs one sample) to multi samples (Ref vs several samles)		** Accuracy can be improved from single(Ref vs one sample) to multi samples (Ref vs several samles).
			*** However false positives (SNP call) would also increase with more number of samples
	** Possible accuracy by read depth based SNP calling is 85%		** Possible accuracy by read depth based SNP calling is 85%
	** '''Possible accuracy by LD (linkage disequilibrium) is >95%'''		** '''Possible accuracy by LD (linkage disequilibrium) is >95%'''
	*** Possible only when multi samples are used		*** Possible only when multi samples are used
	*** Software that uses LD for SNP calling is Beagle, IMPUTE2, QCall, MaCH		*** Software that uses LD for SNP calling is Beagle, IMPUTE2, QCall, MaCH


			=Plan for SNP calling=
			* Assumptions
			** Multiple Genotypes instead of Ref vs One
			** Right combination (contrasting genotype types for specific type ) vs ref.
			** LD based SNP calling
			** Cross check the SNPs against all the 18 genotypes vs contrasting types

2016-05-17T09:22:25Z

Base Calling

← Older revision		Revision as of 09:22, 17 May 2016
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	** Accuracy can be improved from single(Ref vs one sample) to multi samples (Ref vs several samles)		** Accuracy can be improved from single(Ref vs one sample) to multi samples (Ref vs several samles)
	** Possible accuracy by read depth based SNP calling is 85%		** Possible accuracy by read depth based SNP calling is 85%
	** '''Possible accuracy by LD (linkage disequilibrium) is >95%'''		** '''Possible accuracy by LD (linkage disequilibrium) is >95%'''
			*** Possible only when multi samples are used
			*** Software that uses LD for SNP calling is Beagle, IMPUTE2, QCall, MaCH

2016-05-17T09:20:39Z

Base Calling

← Older revision		Revision as of 09:20, 17 May 2016
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	** Hetorozygous -> If an SNP (different than ref) base is counted across the read depth to be less than 80%		** Hetorozygous -> If an SNP (different than ref) base is counted across the read depth to be less than 80%
	** Sequence/alignment Error -> If an SNP based is counted to be less than 10%		** Sequence/alignment Error -> If an SNP based is counted to be less than 10%
			** This is true of the depth is minimum of 20x
			* Accuracy in SNP calling
			** Accuracy can be improved from single(Ref vs one sample) to multi samples (Ref vs several samles)
			** Possible accuracy by read depth based SNP calling is 85%
			** '''Possible accuracy by LD (linkage disequilibrium) is >95%'''