Indel Realignment Implementation

Although global alignment will frequently succeed at aligning reads to the proper region of the genome, the local alignment of the read may be incorrect. Specifically, the error models used by aligners may penalize local alignments containing INDELs more than a local alignment that converts the alignment to a series of mismatches. To correct for this, we perform local realignment of the reads against consensus sequences in a three step process. In the first step, we identify candidate sites that have evidence of an insertion or deletion. We then compute the convex hull of these candidate sites, to determine the windows we need to realign over. After these regions are identified, we generate candidate haplotype sequences, and realign reads to minimize the overall quantity of mismatches in the region.

Realignment Target Identification

To identify target regions for realignment, we simply map across all the reads. If a read contains INDEL evidence, we then emit a region corresponding to the region covered by that read.

Convex-Hull Finding

Once we have identified the target realignment regions, we must then find the maximal convex hulls across the set of regions. For a set R of regions, we define a maximal convex hull as the largest region hat{r} that satisfies the following properties:

\[\begin{split}\hat{r} &= \cup_{r_i \in \hat{R}} r_i \\ \hat{r} \cap r_i &\ne \emptyset, \forall r_i \in \hat{R} \\ \hat{R} &\subset R\end{split}\]

In our problem, we seek to find all of the maximal convex hulls, given a set of regions. For genomics, the convexity constraint is trivial to check: specifically, the genome is assembled out of reference contigs that define disparate 1-D coordinate spaces. If two regions exist on different contigs, they are known not to overlap. If two regions are on a single contig, we simply check to see if they overlap on that contig’s 1-D coordinate plane.

Given this realization, we can define the convex hull Algorithm, which is a data parallel algorithm for finding the maximal convex hulls that describe a genomic dataset.

\[\begin{split}data &\leftarrow \text{input dataset} \\ regions &\leftarrow data\text{.map}(data \Rightarrow \text{generateTarget}(data)) \\ regions &\leftarrow regions\text{.sort}() \\ hulls &\leftarrow regions\text{.fold}(r_1, r_2 \Rightarrow \text{mergeTargetSets}(r_1, r_2))\end{split}\]

The generateTarget function projects each datapoint into a Red-Black tree that contains a single region. The performance of the fold depends on the efficiency of the merge function. We achieve efficient merges with the tail-call recursive mergeTargetSets function that is described in the hull set merging algorithm.

\[\begin{split}first &\leftarrow \text{first target set to merge} \\ second &\leftarrow \text{second target set to merge} \\ \text{if} &first = \emptyset \wedge second = \emptyset \\ &\text{return} \emptyset \\ \text{else if} &first = \emptyset \\ &\text{return} second \\ \text{else if} &second = \emptyset \\ &\text{return} first \\ \text{return}& \\ \text{if} &\text{last}(first) \cap \text{head}(second) = \emptyset \\ &\text{return} first + second \\ \text{else}& \\ &mergeItem \leftarrow (\text{last}(first) \cup \text{head}(second)) \\ &mergeSet \leftarrow \text{allButLast}(first) \cup mergeItem \\ &trimSecond \leftarrow \text{allButFirst}(second) \\ &\text{return mergeTargetSets}(mergeSet, trimSecond)\end{split}\]

The set returned by this function is used as an index for mapping reads directly to realignment targets.

Candidate Generation and Realignment

Once we have generated the target set, we map across all the reads and check to see if the read overlaps a realignment target. We then group together all reads that map to a given realignment target; reads that do not map to a target are randomly assigned to a “null” target. We do not attempt realignment for reads mapped to null targets.

To process non-null targets, we must first generate candidate haplotypes to realign against. We support several processes for generating these consensus sequences:

  • Use known INDELs: Here, we use known variants that were provided by the user to generate consensus sequences. These are typically derived from a source of common variants such as dbSNP (Sherry et al. 2001).
  • Generate consensuses from reads: In this process, we take all INDELs that are contained in the alignment of a read in this target region.
  • Generate consensuses using Smith-Waterman: With this method, we take all reads that were aligned in the region and perform an exact Smith-Waterman alignment (Smith and Waterman 1981) against the reference in this site. We then take the INDELs that were observed in these realignments as possible consensuses.

From these consensuses, we generate new haplotypes by inserting the INDEL consensus into the reference sequence of the region. Per haplotype, we then take each read and compute the quality score weighted Hamming edit distance of the read placed at each site in the consensus sequence. We then take the minimum quality score weighted edit versus the consensus sequence and the reference genome. We aggregate these scores together for all reads against this consensus sequence. Given a consensus sequence c, a reference sequence R, and a set of reads \(\mathbf{r}\), we calculate this score using the equation below.

\[\begin{split}q_{i, j} &= \sum_{k = 0}^{l_{r_i}} Q_k I[r_I(k) = c(j + k)] \forall r_i \in \mathbf{R}, j \in \{0, \dots, l_c - l_{r_i}\} \\ q_{i, R} &= \sum_{k = 0}^{l_{r_i}} Q_k I[r_I(k) = c(j + k)] \forall r_i \in \mathbf{R}, j = \text{pos}(r_i | R) \\ q_i &= \min(q_{i, R}, \min_{j \in \{0, \dots, l_c - l_{r_i}\}} q_{i, j}) \\ q_c &= \sum_{r_i \in \mathbf{r}} q_i\end{split}\]

In the above equation, r(i) denotes the base at position i of sequence r, and \(l_r\) denotes the length of sequence r. We pick the consensus sequence that minimizes the \(q_c\) value. If the chosen consensus has a log-odds ratio (LOD) that is greater than 5.0 with respect to the reference, we realign the reads. This is done by recomputing the CIGAR and MDTag for each new alignment. Realigned reads have their mapping quality score increased by 10 in the Phred scale.