SNP: Difference between revisions
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* 1% error rate | * 1% error rate | ||
* Alignment (Trade off between accuracy and read depth) | * 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% | |||
Revision as of 08:59, 17 May 2016
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%