What happens to heterozygous sites when you go from reference sequence to sequence modified by variants?

Question

[jxiang15]

In a previous post, it was recommended to use either vcftools or FastaAlternateReferenceMaker if you have a reference sequence and a variant file, and you to get a new FASTA file.

However, with the 1000 genomes data, the data is phased. So at heterozygous sites, should the ALT allele be substituted or should the REF allele be left in the sequence?

Thanks in advance

Answer 1

[GouthamAtla]

FastaAlternateReferenceMaker's --useIUPAC option will place the IUPAC code wherever there is heterozygous state.

[jxiang15]

What happens if you don't put that option, what is the default behaviour?