timd1/npore repository overview

npore is a read realigner which recalculates each read's fine-grained alignment in order to more accurately align ''n-polymers'' such as homopolymers (n=1) and tandem repeats (2 ≤ n ≤ 6). In other words, given an input BAM, it adjusts each read's CIGAR string to more accurately model the most likely sequencing errors and actual variants. Traditional affine gap penalties are context-agnostic, and do not model the higher likelihood of INDELs in low-complexity regions (particularly n-polymers), leading to poor or inconsistent alignments. We find that npore improves pileup concordance across reads and results in slightly better variant calling performance.