SNP data in phylip format

Question

[pedroamandrade]

Hi everyone,

I have a SNP database that I want to convert to phylip format (later to use in Lamarc), but every example I have come across is from sequence data. When converting the data with PGDSpider there's an option to write the data as SNP-type, but afterwards the program converts it to sequence-type anyway. Concatenating the SNPs into a pseudo-sequence could be an option, but then Lamarc assumes the loci are linked, which is not the case. Can anyone exemplify how a SNP database in phylip format is organized?

Answer 1

[joana.isabel.meier]

I wrote a python2 script that converts vcf to phylip format. You can download it here: https://github.com/joanam/scripts/blob/master/vcf2phylip.py

usage: vcf2phylip.py [-h] -i <input.vcf> -o <output.phylip> [-r] [-f] [-e] [-m]

For more details see the help message (-h).

Cheers, Joana

[ruyalu0321]

Hi, Joana I want to ask if your script is able to deal with polyploidy samples? I have got a multi-sample vcf from GATK UnifiedGenotyper, and now trying to convert it to phylip format for the following phylogenetic analysis.

Answer 2

[perezalquicira]

Hi, did you find the way to convert vcf file to phylip? I am dealing with the same problem. Does any one have any suggestions to convert vcf to phylip particularly to prepare infile for raxml?

Thanks