Question: How to get per sample read depth from VCF with no DP field
0
gravatar for Rubal
3.3 years ago by
Rubal250
Germany
Rubal250 wrote:

Hello Everyone,

I have a VCF file that has no DP info only AD (allelic depth). Does anyone know of a way that I can get per sample mean read depth using only the AD filter?

I could write a custom script that sums the two AD values for each site, but I'd be more comfortable if there was a standard tool available (and it would save a lot of time).

example for two individuals:

GT:AD   0|1:6,5 0|0:12,0

Thank in advance!

depth coverage vcf • 1.7k views
ADD COMMENTlink modified 3.3 years ago by chen1.9k • written 3.3 years ago by Rubal250
1
gravatar for chen
3.3 years ago by
chen1.9k
OpenGene
chen1.9k wrote:

AD = Allele Depth, is not enough to calculate depth

If you don't have DP, you need RD = Reference Depth

ADD COMMENTlink written 3.3 years ago by chen1.9k

Thanks for the reply that's good to know. Why isn't Allele Depth sufficient, I assumed if you add the counts from both alleles you would get the read depth.

ADD REPLYlink written 3.3 years ago by Rubal250
0
gravatar for chen
3.3 years ago by
chen1.9k
OpenGene
chen1.9k wrote:

Allele Depth is the depth for ALT, and REF is not included

ADD COMMENTlink written 3.3 years ago by chen1.9k
1

This belongs under the comment from @Rubal above.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax71k

I would like to discuss more about the allele frequency spectrum thread at (https://www.biostars.org/p/101218/). Could you share your email address. It would help a lot. Thanks

ADD REPLYlink written 3.1 years ago by hellbio370
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 799 users visited in the last hour