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Table 4 Reduction in called variants by ASDPex

From: Alternate-locus aware variant calling in whole genome sequencing

Variant calling pipeline Total variants Variants per Mb
GRCh37 canonical 114,023 ± 4,983 2198.3 ± 207.6
GRCh38 canonical 120,807 ± 4,069 1975.2 ± 66.5
  1. The variant counts are shown for 121 in-house whole-genome sequencing samples in the ALT-LOCI-containing regions. For GRCh37, a liftover of the regions was performed and region 116 was removed from both datasets, since no alignable region(s) are present in GRCh37. Since the size of the regions is different in GRCh37 and GRCh38, average variant counts per megabase (Mb) are also shown. On average, there was a reduction of 7863 ± 2675 (6.5%) variants called using ASDPex in the ALT-LOCI-containing regions, corresponding to a reduction from 1975.2 ± 66.5 to 1846.7 ± 71.6 variants per Mb