Fig. 2

STRling joint calling workflow. Index: STRling creates an index of the reference genome, recording the genomic coordinates where large STRs are observed. These regions act as STR “sinks”, collecting repetitive reads. Any reads mapping to these regions, in addition to unmapped reads, are candidates to have arisen from a large STR expansion. Extract: STRling counts k-mers to find high STR-content reads, then checks the mate to move the read to its correct position. Merge: read evidence is combined across individuals to increase the accuracy and uniformity of candidate STR expansion loci. Call: STRling estimates the allele sizes using the k-mer count across all reads assigned to a given locus in a linear model. Outlier: STRling checks the distribution across all individuals at a given locus, and tests for outliers