On linux commend line usage for the pipeline, it accepts several formats. I found that a hapmap file has to be in a diploid format.
Simply, it can be converted from a vcf file to a hapmapdiploid with TASSEL5.
"TASSEL5/run_pipeline.pl -vcf yourfile.vcf -export -exportType HapmapDiploid"
And then, try the program.
On linux commend line usage for the pipeline, it accepts several formats. I found that a hapmap file has to be in a diploid format. Simply, it can be converted from a vcf file to a hapmapdiploid with TASSEL5. "TASSEL5/run_pipeline.pl -vcf yourfile.vcf -export -exportType HapmapDiploid" And then, try the program.