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kage-genotyper / kage

Alignment-free genotyper for SNPs and short indels, implemented in Python.
GNU General Public License v3.0
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The quality of genotyping is low #12

Open unavailable-2374 opened 3 months ago

unavailable-2374 commented 3 months ago

Hi

I completed the genotyping of all samples (the previous error was not resolved, so I replaced one of the samples). After merging them, I conducted quality control. Unfortunately, the genotyping quality was very low. I used vcftools with minGQ20 and max-missing 0.8, but in the end, I only got six hundred thousand SNPs, which is obviously lower than the normal value. What could be the problem?

The sequencing depth of the samples was all above 10X.

Best， Shuo

ivargr commented 3 months ago

Hi!

Did you create the index by merging all the chromosome vcfs first?

I have created an index by merging the vcfs you shared with me earlier. I have shared this index and the vcf with you (you should get an email from UIO filesender). Could you try using that index?

unavailable-2374 commented 3 months ago

Hi!

Thank you for sharing!

I have completed the entire genotyping process, including both SNPs and SVs. However, it seems to be inadequate for downstream analysis because when I use these variants for population structure analysis, it doesn’t work, regardless of whether I use PCA or admixture; neither method is effective.

So I guess I have to try anther method to complete my project.

Best Regards, Shuo

On Apr 2, 2024, at 20:07, ivargr @.***> wrote:

Hi!

Did you create the index by merging all the chromosome vcfs first?

I have created an index by merging the vcfs you shared with me earlier. I have shared this index and the vcf with you (you should get an email from UIO filesender). Could you try using that index?

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