According to our evaluations in Fig. 1c, most variants with ‘hap=2’ should be germline-heterozygous variants, while most variants with ‘hap>3’ should false positives. Variants from MuTect2 and GATK haplotype callers all had a large fraction of variants phased to have 2 or >3 haplotypes. MosaicHunter has a ‘linkage filter’ which filters out all variants completely linked with one allele of nearby SNPs, this is the reason MosaicHunter detects less phasable sites and no sites with ‘hap=2’. MosaicHunter does not call variants from RepeatMasker regions, while all other tools call mosaics genome-wide.