Sample quality control¶
For a small proportion of samples, the sequencing data are not of sufficiently high quality to make reliable CNV calls. Sample level quality control is performed based on the number and ratio of different call types and the proportion of common CNVs detected. If CNV data for a proband do not pass this quality control step, the family is flagged in the Interpretation Portal with one of the following flags:
| Flag | Summary | Metrics causing flag activation |
|---|---|---|
poor_quality_CNV_calls |
some of the CNV calls in the sample are expected to be of poor quality | - count of autosomal PASS CNVs ≥ 980 or - Log2(Loss/Gain) < -2.2 |
suspected_poor_quality_CNV_calls |
majority of the CNV calls in the sample are expected to be of poor quality | - count of autosomal PASS CNVs ≥ 195 or ≤ 980, or ≤ 121 or - Log2(Loss/Gain) ≥ -2.2 & ≤ -1.0, or ≥ 0.1 or - fraction of common1 autosomal PASS CNV calls < 0.375 |
-
a CNV is defined as common if it has 50% reciprocal overlap with a CNV from Conrad et al. 2010. ↩