Quality control¶
Genomic sequencing data are subject to a series of QC checks performed by the Genomics England automated pipeline to ensure they are of sufficient quality and are suitable for processing.
The following QC checks are completed as part of the pipeline:
| Quality control | Description |
|---|---|
| Data integrity | md5sum check to confirm integrity of the genomic data transferred from the sequencing provider |
| Genome coverage | 95% of the autosomal genome covered at ≥15x calculated from reads with mapping quality >10 |
| Base quality | >85x10^9 bases with Q≥30 after removing duplicate reads and overlapping bases after adaptor and quality trimming Note: Saliva samples are exempt from this check |
| Contamination | Germline cross-sample contamination performed using VerifyBamID. Samples with >3% contamination are considered as failing. |
Samples not passing these criteria are reported to the NHS GLHs via the Sample Failures Report. Saliva-derived DNA
samples are exempt from the minimum coverage requirement and a flag LOW_COVERAGE will be displayed in the
Interpretation Portal for any sample which does not pass the coverage QC metric (indicated in red box in image below).
