FastaAlternateReferenceMaker -- how to create the two fasta version of a diploid ?
I have been struggling recently with my data. Indeed I have aligned my individuals to a reference fasta and now I have a vcf. Thanks to FastaAlternateReferenceMaker I can generate the alternate reference. But here is my struggle, if I have a SNPs homozigosity thus my fasta reference will differ from the real reference. So that's why I would like to know how to create a fasta including all the genes that include SNPs that have been selected and used for creating the FastaAlternate, and that would be a Fasta non-alternate version...
I thought of selecting the SNPS strongly on my vcf but in that case I will miss all the genes that will be discarded... Any solution for me?
Please let me know,