Unable to run GLM on GBS data for GWAS analysis

[Dr Suran Nambisan]

Dear All

I am running GLM on 97 samples or GWAS analysis, but am getting stuck with the error: no genotype data remained after filtering.

Could you please suggest what can be done?

The command run and the error is copied below:

/apps_940/Tassel_5.0/tasseladmin-tassel-5-standalone-b2457dfa89c7/run_pipeline.pl -Xmx10g -fork1 -h productioHapMap_mseI.hmp.txt -filterAlign -filterAlignMinCount 50 -filterAlignMinFreq 0.05 -fork2 -importGuess Phenotypic_data_GBS_traits2.txt -combine3 -input1 -input2 -intersect -FixedEffectLMPlugin -endPlugin -export gbs_moorthy_minCount50_minMAF05_GLM

 [Thread-6] WARN net.maizegenetics.gui.DialogUtils - No genotype data remained after filtering: Datum

Thanks for your help.

regards

Suran

[Terry Casstevens]

This filter criteria is removing all the data
-filterAlign -filterAlignMinCount 50 -filterAlignMinFreq 0.0

Probably the min count is higher than what your data has

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