issue with setting root

[Safae1501]

Hi, I've been using glactools for a while now, with no issues, to manipulate files and export them to treemix format. Today I was working on a new sheep dataset and encountered a problem when setting the root: glactools replaceanc SM_Sheep_Filtered.acf.gz M-0006.acf.gz > SM_Sheep_Filtered_root.acf.gz

error message: The reference allele differs between NC_019458.2 0 A,G 0,0:0 0,0:0 1,1:0 2,0:0 .... and NC_019458.2 0 G,A 1,1:0 1,1:0

Does anyone know what's the problem here and how can I solve it?

Thanks!

[grenaud]

Hello! it seems that in one file, A is the reference and G is the alternative. The other file has the opposite G is the reference and A is the alternative. So glactools complains because one has to be incorrect.

[grenaud]

just a general question, how come you have a SNP at coordinate 0? Could you please email me the files + full command lines + fai file for the reference genome?

[grenaud]

@Safae1501 Have you had time to send me the files?

[Safae1501]

Thank @grenaud for your interest. As the file I'm working on belongs to an ongoing project, I'm waiting for the PI approval to share it with you, I will do so as soon as I get it.

[grenaud]

Ok I honestly just need about 10 lines around the site that causes the problem.