BQSR Implementation

Base quality score recalibration seeks to identify and correct correlated errors in base quality score estimates. At a high level, this is done by associating sequenced bases with possible error covariates, and estimating the true error rate of this covariate. Once the true error rate of all covariates has been estimated, we then apply the corrected covariate.

Our system is generic and places no limitation on the number or type of covariates that can be applied. A covariate describes a parameter space where variation in the covariate parameter may be correlated with a sequencing error. We provide two common covariates that map to common sequencing errors (Nakamura et al. 2011):

  • CycleCovariate: This covariate expresses which cycle the base was sequenced in. Read errors are known to occur most frequently at the start or end of reads.
  • DinucCovariate: This covariate covers biases due to the sequence context surrounding a site. The two-mer ending at the sequenced base is used as the covariate parameter value.

To generate the covariate observation table, we aggregate together the number of observed and error bases per covariate. The two algorithms below demonstrate this process.

\[\begin{split}read &\leftarrow \text{the read to observe} \\ covariates &\leftarrow \text{covariates to use for recalibration} \\ sites &\leftarrow \text{sites of known variation} \\ observations &\leftarrow \emptyset \\ \text{for} &base \in read \\ &covariate \leftarrow identifyCovariate(base) \\ &\text{if isUnknownSNP}(base, sites) \\ &observation \leftarrow Observation(1, 1) \\ &\text{else} \\ &observation \leftarrow Observation(1, 0) \\ &observations.\text{append}((covariate, observation)) \\ &\text{return} observations \\\end{split}\]
\[\begin{split}reads &\leftarrow \text{input dataset} \\ covariates &\leftarrow \text{covariates to use for recalibration} \\ sites &\leftarrow \text{known variant sites} \\ sites.\text{broadcast}() \\ observations &\leftarrow reads.\text{map}(read \Rightarrow \text{emitObservations}(read, covariates, sites)) \\ table &\leftarrow observations.\text{aggregate}(\text{CovariateTable}(), \text{mergeCovariates}) \\ \text{return} table\end{split}\]

The Observation class stores the number of bases seen and the number of errors seen. For example, Observation(1, 1) creates an Observation object that has seen one base, which was an erroneous base.

Once we have computed the observations that correspond to each covariate, we estimate the observed base quality using the below equation. This represents a Bayesian model of the mismatch probability with Binomial likelihood and a Beta(1, 1) prior.

\[\mathbf{E}(P_{err}|{cov}) = \frac{\text{errors}(cov) + 1}{\text{observations}(cov) + 2}\]

After these probabilities are estimated, we go back across the input read dataset and reconstruct the quality scores of the read by using the covariate assigned to the read to look into the covariate table.