Table 5 Quality metric conditions for samples to pass quality control.

From: The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly

Metric

Initial QC (Infinium SNPs)

Final QC (full genotypes)

Call rate

>0.98

>0.98

Depth standard deviation

<10

<10

VAF standard deviation at loci called heterozygous

<1

<1

Heterozygous:homozygous variant ratio

<2

<2

X chromosome inbreeding coefficient

<0.2 or >0.8

Not tested

Singleton rate

<0.001

Not tested

  1. Two rounds of quality control (QC) were performed, with different metric cutoffs: a first round based on genotypes at Illumina Infinium QC Array 24 SNPs only and a second round based on genotypes called across the whole-genome. Only samples passing all cutoffs in both rounds were included in the MGRB Phase 2 release
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