Error: null during running MLM at TASSEL

[Manoj Kumar]

Hi,

I got an issue during the run MLM at TASSEL. I got GLM successfully however once I go for MLM, it shows null error. I am using MDS with number of axes 6 and then Data/Intersect Join to generate population. Furthermore, I am using Kinship method with Max allele 6. Please see some of the pics attached.

Help me!!!!!!!!!!!

regards,

[kpoviessi akovognon]

Hi,

Maybe, watch this Tassel workshop on YouTube, very informative.

TASSEL Workshop Part 2: LD, PCA, Kinship, and GWAS 

Regards,

[Peter Bradbury]

It is likely that you have one or more non-variant SNPs. Sometimes they show up after joining the phenotypes and genotypes because some taxa in genotypes do not have phenotypes. What you should do is to filter on minimum allele frequency (try 0.05) after intersect joining the phenotype and the genotype. If that does not solve the problem follow the instructions in "Reporting TASSEL 5 issues" at https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf. 

[Manoj Kumar]

Thank you for providing me the link. It is really helpful.