SNP

SNP Filtering Plans

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