Replacing SNP positions with IUPAC code in FASTA

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9.1 years ago

hpapoli ▴ 140

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,

SNP fasta iupac • 2.7k views

ADD COMMENT • link updated 22 months ago by Ram 43k • written 9.1 years ago by hpapoli ▴ 140

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what's your input format ? how us teh file. Are all your variants real SNPs ? (no indel)

ADD REPLY • link 9.1 years ago by Pierre Lindenbaum 161k

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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.

ADD REPLY • link 9.1 years ago by hpapoli ▴ 140

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Oh, Yes, all variants are SNPs, no indels.

ADD REPLY • link 9.1 years ago by hpapoli ▴ 140

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