File importing issue

[adithya p balakrishnan]

Hi all,

I'm new to TASSEL and having trouble loading a HapMap file in version 5. I've checked the format and values multiple times but still get an error.

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

Best regards,

Adithya

[Hugo Cuevas]

The SNPs in each chromosome must be in acending order. You need to sort the SNPs for each chromosome.

Best,

Hugo

--
You received this message because you are subscribed to the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
To unsubscribe from this group and stop receiving emails from it, send an email to tassel+un...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/tassel/be44ea08-3146-4648-96a7-7bd62456bfdbn%40googlegroups.com.

[adithya p balakrishnan]

Thanks for getting back to me. 

Just to be sure, when you say SNPs, do you mean their ID or the type of SNP? 

I need to sort each chromosome by either the '#rs' column (1st column) or the 'allele' column (2nd column).

Best regards,

Adithya

To view this discussion visit https://groups.google.com/d/msgid/tassel/CADk-H2X0ENojsAZQ9sm2WVSf54eXyKAiPyE3syCoJG%2Br6LJGHA%40mail.gmail.com.

[adithya p balakrishnan]

Hello Hugo,

I've followed your advice and the TASSEL manual by sorting the data first by chromosome and then by position. I've also changed the genotype nucleotides to a two-letter (diploid) format (e.g., AA for A).

However, I'm still encountering the same error when trying to load the data: 

"Error:BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values."

Could you please provide further assistance?

Best regards,

Adithya

On Sun, Jun 22, 2025 at 6:03 AM Hugo Cuevas <hecue...@gmail.com> wrote:

To view this discussion visit https://groups.google.com/d/msgid/tassel/CADk-H2X0ENojsAZQ9sm2WVSf54eXyKAiPyE3syCoJG%2Br6LJGHA%40mail.gmail.com.

[Terry Casstevens]

This error also indicates that your number of samples doesn't match
the number of genotype values. Make sure this is a tab-delimited file,
and doesn't have spaces anywhere

On Sun, Jun 22, 2025 at 6:43 AM adithya p balakrishnan

> To view this discussion visit https://groups.google.com/d/msgid/tassel/CAF98oegnZz0biS9r-12Hah%3DLWaQuPwXjK0-vbR%2B9JobmNWEHwg%40mail.gmail.com.

[Hugo Cuevas]

By Chr..and within chromosome by position

To view this discussion visit https://groups.google.com/d/msgid/tassel/CAF98oeg1EV%2B-r%2BGJ%2BH98cGjFi%2BHvYRuz_uKNjt%2B6ER1WmxTkbw%40mail.gmail.com.

[adithya p balakrishnan]

Thank you. It worked!

To view this discussion visit https://groups.google.com/d/msgid/tassel/CADk-H2XCT0RwV_Z-FUB_sQgELZZLukQD3c44pmSmNSB2Lr4m8Q%40mail.gmail.com.

[adithya p balakrishnan]

Thank you so much. My data heads had spaces. 

After removing, now it's successfully imported into TASSEL5.

Best regards,

Adithya

To view this discussion visit https://groups.google.com/d/msgid/tassel/CACHsrTsmfxPFDg0cxJXruYwbb%3DaJVXOqTC-%2BeHNd4xJGwOd%3DHA%40mail.gmail.com.