Compute Phylogenetic Trees Using Snps Data (VCF files)

Question

[JJ]

Hi all,

I was wondering wether there are any new tools to construct phylogenetic trees using SNPs, in particular based on VCF files. I came across three tools/packages SNPYHLO, snpTree and SNPRelate.

I cannot get SNPYHLO to work - keeps throwing errors (maybe because I work with a non-model organism) and the documentation is very limited. snpTree requires read files and/or assembled genomes instead of vcf files. SNPRelate works (yeah!); however, I would like to confirm the results with another tool and also try to make a prettier plot. Any suggestions?

I found a couple of old posts like this one but I wondered if there really aren't any new tools out that simplify the task.

Thanks!

[princy149]

read its manual first and if you have problem then let me know..i will explain you steps..

[JJ]

Hi again :) so I've imported my VCFs and ran the Cladogram function. Now I would like to refine it: first with filtering and then with LD There is some information about filtering in the youtube video - something I still have to figure out. Do you have some tips? I have cell line data. Most importantly, however, I could not find anything on how to use a pruned set of SNPs for the computation of the Cladogram. Could you help me here? Thanks!!!

[princy149]

hi, i did it by myself in my project so have no idea about you tube but i want to tell you something of using TASSEL 4.3 and TASSEL 5, in case of 4.3 version you do not have to need convert your vcf data into sort-genotype file but if you will use TASSEL 5 then it need to first convert your vcf data as "sort-genotype data". beside this, you want to know about filtering, so give you some idea as...there is some options as: sites , sites name, taxa name, traits so you can filter your data according to your choice, here Site means "SNPs" which are present in your vcf data or any other data format as "Hapmap". so for this after loading your data, go to filter options and click on your vcf data file,( best is if you convert your vcf data into hapmap data as export option in Tassel).. will give you more info later.... please first try to make "sort-genotype file" using your data..in tassel 5..( if you didnt done this)

[JJ]

Hi, I have imported and sorted it already - that's all done. I also made a Cladogram but I could not find anything on how to use a pruned set of SNPs for the computation of the Cladogram - so how can I use the LD for the cladogram? Thanks :)

[princy149]

Hi, do you want to make LD for your snps data? I didn’t understand your question clearly but if you want to make LD for your data via TASSELS then choose chromosomes filter using its start site position and end site position which may be shown in your TASSELS, choose data for individual chromosomes numbers and go for LD and check LD graph in results. You can also check you data with Haploview for block estimation of your SNPs data. If you want some different things then please clarify me your question.

[JJ]

Hi, Sorry for not being clear... I read that it it is important to use a pruned set of SNPs which are in approximate linkage equilibrium with each other to avoid the strong influence of SNP clusters in relatedness analysis (see here) so I wondered how I can do this in TASSEL. So, is there a way to do reduce SNP redundancy by linkage disequilibrium (LD) in TASSEL? Thanks :)

[Denis]

I'm looking for the similar software, but i need a tree with bootstrap supports. Do you know any ready solution? Tassel doesn't do that unfortunately.

[JJ]

Hey, actually I haven't gotten around to continue on this project but I will pick it up in the next couple of weeks.

However, as written above I've used SNPRelate, which works. Give that one a try. I would have liked a second tool to confirm it but haven't found any. Have you tried out any tools?

[Denis]

Hi, i'm curious,if the SNPRelate will give bootstrap values along with a tree? If i'm correct i tried a SNPhylo several years ago, but was not able to get any tree. Recently i've converted VCF file to Hapmap and then by means of R/Bash scripting converted it to the fasta alignment eventually. Since that moment it's posible to use any standard software for phylogeny inference. But i'm not sure that it's the best approach.

Answer 1

[princy149]

Hi J J,

If you want to create SNPs phylogenetic tree via Vcf files , then you can try TASSELS tool through which you can get more clear images of phylogeny tree.

[JJ]

Could you add a link to the tool? Thanks!!

[Ram]

I have edited your post and added the link. Please do not add multiple answers when the right thing to do is editing an existing answer and adding/changing content in there.

Answer 2

[sankar2004]

Use the simple one-click software VCF2POPTREE

[Ram]

Please create a TOOL type post featuring your tool. Do not spam multiple posts with links to your tool, especially when the links look suspicious (not GitHub, not even a formal webpage describing the tool). Such repeated spamming will result in account suspension.