SNP file format detection and its VCF conversion

Question

[arnstrm]

Hi all,

I am having trouble identifying the file format for the SNPs. Does anybody know what format this is? Is there any program that can convert this format to VCF? Any help will greatly be appreciated!

(if it helps, the file was downloaded from Soybase: see last section)

The file looks something like this:

Answer 1

[Devon Ryan]

That's not any standard sort of format, so it's highly unlikely that a pre-made converter exists. Having said that, depending on your background it might not be that difficult to write something to do the conversion. A bit of python with pysam (or anything else that allows querying a fasta file for the sequence at a given position) should work.

[arnstrm]

Thanks for the reply. Yes, I'm considering it, but I need to know info such as reference/alternate base in the above file, if it is phased or unphased etc. Do you have any idea?

[Devon Ryan]

It's presumably unphased, but you'd really have to ask the person who produced it. I'll also note that there's no apparent indication of whether a sample is homo or heterozygous (I have no idea what the ploidy of this species is).