Open Lucio-Yang opened 11 months ago
The "." means "missing genotype". For some reason, vg
was not able to genotype the site. Usually, it is due to a missing alignment, but I suppose complex graph structures could put vg
in difficulty as well.
The "." means "missing genotype". For some reason,
vg
was not able to genotype the site. Usually, it is due to a missing alignment, but I suppose complex graph structures could putvg
in difficulty as well.
Thank you for your quick reply ! I still have a question: can the tanslocation or inversion be reflected in the graph or VCF obtained by PGGB, and how to count it?
You will see both of them in the graph. In the VCF, you can see the inversions after VCF decomposition with vcfwave
. You can trigger the decomposition specifying the max allele length with the -V
option (something like -V reference:10000)
.
Hi, I ran PGGB to build a pan-genome map of wheat and got a VCF file. I want to know what “.” in the VCF represent. If “0” represents consistency with the reference, then what does “.” represent? Is this site not aligned after multiple sequence alignment?
Thanks !![image](https://github.com/pangenome/pggb/assets/42206757/0f18cde3-8f7b-4f1b-b5b3-e5b85a8fa5e0)