Step 7: Review quality metrics of processed data

After the sample get processed by VCPA, users can review the sample level stage-by-stage quality metrics of the VCPA pipeline via the tracking database.

The tracking database can be accessed using the below endpoints (where IP is the public IP address of the tracking database)

1) To view the list of projects: http://IP/v1/projects

2) To view the samples information with each of the projects:

http://IP/v1/sample/details?project_id=*

(where * is the project_id)

VCPA is divided into 4 stages at the per sample level (see overview figure in the Introduction session for details). For each stage of VCPA, the quality metrics can be accessed respectively as follows:

3) Stage0 - http://IP/v1/stats/stage0/project_id=*

4) Stage1 - http://IP/v1/stats/stage1/project_id=*

5) Stage2a - http://IP/v1/stats/stage2a/project_id=*

6) Stage2b - http://IP/v1/stats/stage2b/project_id=*

(where * is the project_id)

Notable metrics:

Sequencing coverage – Sequencing coverage describes the average number of reads that ‘align’ or ‘cover’ known reference bases. This coverage level helps determine whether variant discovery can be made with a certain degree of confidence at a specific base location. Coverage metrics are captured at stage1 of VCPA.

Average coverage equation - The WGS depth of coverage calculation is performed using sambamba. We extract the read count and coverage across several percentages. The average depth of coverage for WGS is calculated as: the average chromosome read count * read size summed, divided by number of non-N nucleotides.

Transition to Transversion (Ti/Tv) Ratio – Ratio of the number of transitions (changes from A <-> G and C <-> T) to the number of transversions (changes from A <-> C, A <-> T, G <-> C or G <-> T) for a pair of sequences. It is one of the metrics to evaluate the quality for the callset. Ti/Tv ratio are captured at stage2b of VCPA.

GATK VariantEval is used to calculate the Ti/Tv ratio. Database also capture number of known and novel Ti and Tv SNPs.