# Creating consensus fasta using iupac codes

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Fasta files can be generated from vcf calls. There are two ways of doing that: (1) concatenate snips together (this can be done using either variants only or calling monomarphic (hom ref) variants as well and concatenating them too); (2) use reference genome as a backbone and incorporate variants into the reference. To incorporate information about heterozygotes, IUPAC substitution codes can be used. Here is a collection of scripts available:

#### Using fasta reference

• the best and most convenient way: (allows to choose a sample from multiVCF and BED mask)
bcftools consensus --iupac-codes --sample --mark

• vcf2fasta.py - phased only
• For GATK fans: FastaAlternateReferenceMaker.

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