Use of Loter in haploid organisms

[pabloangulo7]

Hello,

I would like to ask if it is possible to use loter with haploid organisms, and if so, what parameters need to be adjusted or modified to perform such analysis. On the other hand, I have VCF files containing SNP information for different samples, how could I obtain the haplotype matrices for these haploid organism samples? Finally, would it be necessary to perform linkage disequilibrium prunning of the SNPs before using the program?

Thanks

[gdurif]

Hi, sorry for the late answer.

You can use Loter on haploid organisms. The only constraint it to NOT use the phase correction module, which means:

• with the command line tool, you should NOT use the -pc option (see README for details or run loter_cli -h).
• with the python package, see section III.b in this notebook.

To format your VCF data for Loter:

• in Python see section II.b in the previous notebook.
• with the command line tool it should work if you have a VCF file for each reference population and one for the admixed individuals (see README, replacing the npy input files by vcf files should work).

Regarding the linkage disequilibrium prunning of the SNPs, it should not be necessary. Loter exploits the fact that consecutive SNPs are likely to be inherited from the same parent.

Do not hesitate if some points are not clear or if you have any further question. Best

[pabloangulo7]

Thank you very much. I will try to do it following your advice and report back later. Congratulations for this great tool.

Best