Replacing SNP positions with IUPAC code in FASTA
Hello,
I have called SNPs from pooled data so my genotypes are in the form of a tetraploid or hexaploid such as 0/0/0/1. I want to replace the position of the SNPs with the IUPAC code in the fasta file. I wanted to use the GATK FastaAlternateReferenceMaker but it requires the genotypes to be diploid, how could I solve this problem?
Thanks in advance,
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what's your input format ? how us teh file. Are all your variants real SNPs ? (no indel)
My input format is a typical vcf format, and a typical fasta format. However, after searching a lot, I have decided to write my own python script now as then I can use a simple tab separated file for my SNPs instead of the vcf format.
Oh, Yes, all variants are SNPs, no indels.