Table 2 Comparison of variants called using hg19 and hg19KIndel before and after lifting over the coordinate of variants
From: hg19KIndel: ethnicity normalized human reference genome
Sample | Variant class | Total Calls (hg19) | Total Calls (hg19KIndel) | Overlap | |
|---|---|---|---|---|---|
Before Liftover | After Liftover | ||||
In house whole exome sequencing sample (WES) | SNP | 45,285 | 33,676 | 34 | 30,563 (68%) |
INDEL | 4741 | 3494 | 9 | 3090 (65%) | |