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jiabowang / GAPIT

Genome Association Predict Integrate Tools
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Error in count.temp[, 2] : subscript out of bounds #146

Open emmahovhannisyan22 opened 1 month ago

emmahovhannisyan22 commented 1 month ago

I'm getting the error Error in count.temp[, 2] : subscript out of bounds

while doing GWAS with InDel data. The updates don't seem to be helping. How should the input hapmap data look like to not get this problem?

Thank you.

yaoxkkkkk commented 1 month ago

Hi I had similar problem with you, I use a hapmap converted by vcftools, resulting a "-" standing for indel, and here is jiabo's mail reply:

The problem is not in the Indel. It is matter with the “NA” values. You can replace “-“ to other genotype, such as “Z”, that indicate Indel and rather then missing value. And remove that NA lines. That should work for your converting.

emmahovhannisyan22 commented 1 month ago

Hi, thank you! It doesn't give the error when I convert all ''-'' and "N"s to "Z". Hope the logic remains correct.

yaoxkkkkk commented 1 month ago

Z is commonly used to denote indels, and it's uncertain if converting N to Z will affect your results. You may consider imputing your VCF using tools such as Beagle5 to address NA values.