Question: SNP data in phylip format
0
gravatar for pedroamandrade
4.7 years ago by
Portugal
pedroamandrade40 wrote:

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?

snp phylip • 4.0k views
ADD COMMENTlink modified 2.6 years ago by joana.isabel.meier0 • written 4.7 years ago by pedroamandrade40
0
gravatar for perezalquicira
4.3 years ago by
perezalquicira10 wrote:

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

ADD COMMENTlink written 4.3 years ago by perezalquicira10
0
gravatar for joana.isabel.meier
2.6 years ago by
joana.isabel.meier0 wrote:

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

ADD COMMENTlink modified 2.6 years ago by GenoMax92k • written 2.6 years ago by joana.isabel.meier0

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.

ADD REPLYlink written 24 months ago by ruyalu03210
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