Fig. 4.

Example of misalignment around chr1:26608841 in CHM1. The truth allele is derived from local assembly. Three erroneous read alignments and their correct alignments are shown below it. Each of the three reads is an exact substring of the truth allele, but their alignments are different. The first read ‘errRead1’ is aligned without gaps, as the 3′ end of the read is a substring of the 18 bp deletion. Read ‘errRead2’ is aligned with a 6 bp insertion, as this alignment is better than having two long deletions. Read ‘errRead3’ is also aligned without gaps but with seven mismatches. It is possible for an aligner to find its correct alignment given a small gap extension penalty. On this example, Bowtie2 did not align any reads with gaps. BWA-MEM aligned four reads correctly. Except HaplotypeCaller which locally assembled reads, other callers all called multiple heterozygotes around this region