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2016-06-23T08:39:07Z

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Raj at 03:24, 2 June 2016

2016-06-02T03:24:31Z

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[[Category:Readings]] [[Category:Rajkumar]] [[Category:Biology]]

=Base Calling=
* Minimum Read depth
* Based on Phred scores
* 1% error rate
* Alignment (Trade off between accuracy and read depth)
* Recalibration of Pherd scores
** 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

= 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%
* 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%
* 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).
** 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 LD (linkage disequilibrium) is >95%'''
** Possible only when multi samples are used
** 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
* 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)

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

SNP - Revision history

Raj: 1 revision imported

Raj at 03:24, 2 June 2016