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pkalbers / geva

Genealogical Estimation of Variant Age (GEVA)
MIT License
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Position not viable? #3

Open hsiehph opened 5 years ago

hsiehph commented 5 years ago

Hello,

I tried to use geva to estimate the ages of some rare variants but got empy output. When checking with the log file, I noticed it saying Position not viable. I am not sure what that means and how to resolve this issue. The data set includes ~3000 samples and I am looking at a 1Mb region with >57000 SNVs.

Any idea?

Thanks,

Lsegurel commented 3 years ago

Hi,

I have a similar issue, I only have few (around 10) SNPs in the output and the rest (nearly 1M SNPs) appears as "Positions not viable". Did you manage to resolve this issue ?

Thanks.

erikenbody commented 2 years ago

I found the same problem. The issue seems to be that if your positions file has a position not in your vcf, then the software won't run any sites. This doesn't seem to be the intended behavior, as it should be possible to run the remaining sites. A bandaid solution is to remove those positions that aren't in the VCF

mas-agis commented 1 year ago

I have the same problem. I have several SNPs with 'positions not viable' in the output. The problem is these SNPs were not in the list of markers in the geva format. So the problem is in conversion from phased vcf to geva_format. in my case, 434167 in vcf and only 377661 in the converted one.

xxYaaoo commented 10 months ago

Hello, I have the similar problem. My vcf file and marker.txt file from conversion step contained the same SNPs (and my focal site also in the marker.txt file..). It seemed that all the output files of conversion step were correct, while the "Positions not viable" appeared in the second step when I used that focal site as --position input. Any idea to solve this issue?