Hap map

[Udaya bhanu Angirekula]

Hi all,

I’m new to TASSEL and facing difficulties loading a HapMap file in version 5. Even after checking the format and values several times, I still encounter an error. I can open the .txt file in TASSEL, but I’m unable to convert it into a .hmp.txt file.

I've attached the file and a screenshot. I'd be grateful for any assistance.

Best regards
Uday

[Dongliang Wu]

Replace “NA” with “NN” for missing genotypes in the HapMap file. Ensure all genotypes use 1 or 2 valid letters (A, C, G, T, N, etc.) and each site has the correct number of values matching the samples. 

This is the suggestion from AI.

It might be your missing genotypes coded as NA not NN.

[Dongliang Wu]

I checked my hmp.txt file. TASSEL uses single letter coding for the genotypes like A or T. You might need recode your genotype from two letters to one letter.

On Thursday, September 11, 2025 at 8:25:58 AM UTC-4 Udaya bhanu Angirekula wrote:

[Terry Casstevens]

That message indicates that all your genotypes should be either 1 character value or 2 character. You can't have a mix. And the number of genotypes should match the number of taxa

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[Brandon Monier]

Additionally, if you are interested in retaining multi-allelic information (e.g., a C ref allele and A,G,T alt alleles), a VCF file is a much better format to consider:

https://samtools.github.io/hts-specs/VCFv4.2.pdf