query related to GWAS analysis using Tassel for paired-end GBS data

[Dr Suran Nambisan]

Dear All

Could you suggest how I can use paired-end GBS data for GWAS analysis using Tassel?

Tassel-GBS v2 pipeline gives vcf / hmp output for each read (forward/reverse). SNP output (genotypic file) has data for samples as Amber_1 and Amber_2, whereas I have phenotypic data for sample names, such as Amber.

Could you suggest how I can make use of paired-end SNP output (hmp.txt) for GWAS analysis using Tassel?

Could you also suggest alternatives (softwares/tools/methodology) to solve this problem?

Thanks and regards

Suran