Hi all,
I have a multi-sample vcf file of 350 loci spread across the genome from 85 individuals. I want to use this to ultimately build phylogenetic trees. For this i want to first make fasta sequences of 100kb length for each of the 350 loci for the 85 individuals, something similar to what GATK FastaAlternateRefrenceMaker does. I don't know how to specify sequence length in this tool though. Is it even possible to do what I am trying to do using this tool or any other tool? I would like some suggestions on how to take care of this.
Thank you.
•
written
by
shreyasibiswas88 •
1 answer
I don't know if your approach for phylogenetic trees with fragments like that makes sense, but I'll leave that to others.
How I would handle your project:
- Use the VCF and GATK FastaAlternateRefrenceMaker to make a fasta file per individual
- Make a bed file for each locus (100kb per interval)
- Use bedtools getfasta to slice out your 100kb fragments from the fasta files
Log in to answer this question.
-
Mapping taxa with moderate to sparse loci coverage to reference backbone tree
written by katstancity •
-
How to create a phylogenetic tree
written by anna •
-
Program to run analysis of 60,000 16S sequences?
written by prfsullivan •
-
Best method for phylogeny on bacterial genes
written by vujex •
-
Phylogenetic tree for 16s sequences in a metagenomic data set
written by surathsanda •
-
How do I decide between building a kmer-based or snp-based tree?
written by gatheringdusthere •
-
2/50 inidividuals show missing data at almost all positions in final vcf generated using HaplotypeC…
written by shreyasibiswas88 •
-
Correspondence between unlabeled/different tips of different phylogenetic trees
written by rfm •
-
Phylogenetic Tree to compare my sequences to a database
written by Neuls •
-
Multi-Sample Vcf To Phylogenetic Tree.
written by William
You could make the fasta files and then trim them to be of the length you want. 100kb sounds long if you are going to try and build phylogenetic trees.