Question: gnomaAD exome and genome AF differences
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gravatar for cocchi.e89
5 weeks ago by
cocchi.e8910
cocchi.e8910 wrote:

Hi all,

maybe it is a silly question but in my university script to annotate variants I have a couple of options relatives to gnomAD filtering:

--gnomad-exome-af: is to specify a threshold and it will require variants to pass the threshold in all populations from "--gnomad-exome-pop"

--gnomad-genome-af: is to specify a threshold and it will require variants to pass the threshold in all populations from "--gnomad-genome-pop"

what is exactly the difference amongst these? Are the exome AF relatives only on patients that dis a whole exam sequencing while the "genome" refers to all samples (or only to those who had genome sequencing and not exam seq)

Thanks a lot in advance for any help!

gnomad genome exome • 118 views
ADD COMMENTlink modified 5 weeks ago by Pierre Lindenbaum117k • written 5 weeks ago by cocchi.e8910

I think the gnomad-exome dataset includes AF from exome sequencing datasets only, such as ExAC or ESP6500, whereas gnomad-genome would include AF by counting alleles from WGS datasets as well.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by RamRS20k
0
gravatar for Pierre Lindenbaum
5 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

there are exome and genome data in gnomad.

There are distinct values for the frequences (AF) of each method because there are different arctefact/samples for each method. e.g:

http://gnomad.broadinstitute.org/variant/1-120457932-C-T exome AF: 0.00007992 genome AF : 0.00006368

ADD COMMENTlink written 5 weeks ago by Pierre Lindenbaum117k

Thank you Pierre! Would one would you recommend to choose in order to take only rare variants?

ADD REPLYlink written 5 weeks ago by cocchi.e8910

Would one would you recommend to choose in order to take only rare variants?

no, it depends of the nature of the disease.

ADD REPLYlink written 5 weeks ago by Pierre Lindenbaum117k

Thanks Pierre, can you be more exhaustive about that? As example, if I should analyze IgAN nephropathy which one would you suggest and why?

Thanks a lot again

ADD REPLYlink written 5 weeks ago by cocchi.e8910

I'm not a clinician + I don't know that disease.

You should work in pair with an expert of the disease.

ADD REPLYlink written 5 weeks ago by Pierre Lindenbaum117k
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