SNP file preparation for genotyping

Question

[hpapoli]

Hello,

I am going to prepare a set of SNPs for genotyping by GoldenGateAssay.

The format of the file required is as follows:

SNPname1       ..............ATWCCCAT[C/T]GCCTATTGG..................

And it has been indicated that any SNP in the flanking sequence should be coded by the IUPAC ambiguity codes.

I have a file with a set of my SNPs and I am going to extract the sequences from my FASTA file using the following command in bedtools:

bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]

However, two things remain unclear to me:

1. How should I turn any SNP in the flanking region into an IUPAC code?
2. How should I specify the SNP position like [C/T]?

I was wondering if there is any available tools for this purpose or I should go on trying to develop my own scripts for that.

Thanks in advance

[SS]

Hi hpapoli,

I also need to do the task as you describe above. If you got that working could you please share the script/solution for extracting sequences around target SNPs and also adding IUPAC codes for the SNPs in the flanking regions.

Regards
SS