Question: How to build a phylogenetic tree using fasta obtained from VCF file?
0
gravatar for rimgubaev
14 months ago by
rimgubaev180
Russia/Moscow/Skoltech
rimgubaev180 wrote:

The problem is as follows: I got VCF file obtained by GATK for 288 individuals, then I convert it to nucleotide fasta (using PGDSpider) so the length of individual's fasta sequence corresponds to the number of SNPs in VCF file. If I want to use MEGA to build a tree I first make an alignment which adds gaps that are actually are not in favor in that case. So the question is how to make an alignment file (*.meg) without gaps in order to make a tree in MEGA?

population genetics mega vcf • 861 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by rimgubaev180
1

Not a direct answer but I have used this software (snpphylo) with good results http://chibba.pgml.uga.edu/snphylo/

ADD REPLYlink written 14 months ago by microfuge1.6k

That's pretty close to what I what to do. I think I'll try one. Thanks!

ADD REPLYlink written 14 months ago by rimgubaev180

Hi , I m not sure to understand " so the length of individual's fasta sequence corresponds to the number of SNPs in VCF file" , do you have an example ?

Best

ADD REPLYlink modified 14 months ago • written 14 months ago by Titus910
>individual1
ACGTNGCT
>individual2
AGGTAGNT
>individual3
GCGTAGCT
etc.

The letters correspond to the allele in a certain position. So the sequences are already aligned if it can be said in that situation.

ADD REPLYlink modified 14 months ago • written 14 months ago by rimgubaev180

Ok so i don't understand, why you don't want gaps ?

ADD REPLYlink written 14 months ago by Titus910

Because a letter represents a certain (fixed) position in the genome. For instance, the second letter in the above example is in the 13th chromosome (pos 156) and third is on chromosome 3 (pos 19909). They cannot be moved. I'm sorry for the not clear explanation.

ADD REPLYlink written 14 months ago by rimgubaev180
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