Depth of coverage

[pc2001]

Alex,

Is there any proposal to also include the depth of coverage statistics in the summary output?

thanks!!

[akotlar]

Pankaj,

I think we should include that information. To store the site-level depth (total depth) is simple, if it is provided in the VCF file (DP field). I added an issue to bystro-vcf to do so.

To store the data per-sample is harder, because it would probably require us to add a large amount of information to the output.

• Would we want that information within the annotation output, or as a distinct file?

• If a distinct file, how should we handle search indexing?

For per-sample information, I think we may be moving to a separate output, and allow users to search both the sample-level output and the variant-level (current annotation) output.

Would you be interested in helping me work through the per-sample question together with Cristina?

[pc2001]

Alex,
Would definitely be v. helpful to store the site level info in the annotation file!

Sure, let me know how I can help!