I have a hapmap file from tassel and I want to convert it to a vcf. Tassel can convert the file but takes the major allele as the reference and the minor as the alternative.
I want to use the reference genome for the reference alleles and set the alleles different from the reference genome as the alternative. I also tried GATK but it gives me the error NULL alleles are not supported.
My hapmap file looks like this and is tab deleimited:
rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode sample1 sample2 sample3 sample4 sample5 sample6 sample7
S1_134 C/T 1 134 + N N N N N N C C C N N C C
S1_204 G/A 1 204 + N N N N N N G G R N N G G
S1_340 C/T 1 340 + N N N N N N C C C N N C C
S1_477 C/T 1 477 + N N N N N N C C Y N C C C
There is a tool to perform what I want?