Homozygous reference and alternate alleles reversed

[James Coleman]

Hi All,

I'm working with vcf files generated with VCFv4.2 specifications and have been able to perform all necessary functions for comparison/combination of multiple vcf files (all same reference) in TASSEL 5.2.90, but every time there is an alternate allele representing more than 50% of the total genotype at that position, TASSEL reverses the reference and alternate allele, to give the opposite genotype.  All unique homozygous alternate positions are shown as homozygous reference and homozygous reference are shown as alternate.  Is there a way to make sure the reference and alternate allele stay in the order specified in the vcf files when there are more alternate alleles than reference?  Thank you in advance for any help.