Getting this information from WGS

Question

[zizigolu]

Hi

I have a set of .vcf files from WGS, I have been asked about the sequencing depth of this data

Can I know what is the sequencing depth from .vcf files?

Answer 1

[morovatunc]

The cleanest way would be getting bam file and calculating average read depth.

If you dont have an access to this, variant callers provide depth value. So my suggestion would be to parse that each call in the VCF to calculate average. But I would be careful while doing this because callers usually report the number of reads which passes all of their quality filtration.

If you are going to the second method, please first couple lines of your vcf so that we can see the header + call information. Unfortunetly not all callers are same.

For your future questions, if you are asking a question regarding a vcf, its usually cleanest to share some part of it so what we can help you faster and cleaner.

Cheers!