I have a VCF file with unphased genotypes. I would like to analyze LD, which I understand is best done with phased genotypes, and hence phased haplotypes. I would like to generate a new VCF file with the genotypes in phased format (which would be indicated by the genotypes appearing like 0|1 instead of 0/1). Can anyone suggest a good tool, for any operating system, that can do this?
The newest version of BEAGLE can directly read VCF input files.
Also, our free Mega2 software can read VCF as input and convert to a variety of formats. See http://watson.hgen.pitt.edu/mega2.html for more detail.
You can use p-link (http://pngu.mgh.harvard.edu/~purcell/plink/) or R package for your work.
I suggest BEAGLE version 4. See the web page for the manual and download.
http://faculty.washington.edu/browning/beagle/beagle.html
thank you for the suggestions - they both appear appropriate but can you confirm that plink can read a VCF file as input?
The newest version of BEAGLE can directly read VCF input files.
Also, our free Mega2 software can read VCF as input and convert to a variety of formats. See http://watson.hgen.pitt.edu/mega2.html for more detail.
- is this ok to manipulate the VCF file and create the new column of the genotype?
- Suppose I am attaching the vcf file in which GT value not present. Then how we will calculate the GT value?
A bit late but for future researchers, I have just used a tool called shapeit that can produce vcf files with phased genotypes (0|1 instead of 0/1).
It is a bit tricky to use if there are parts in your genome or parts of your loci that are missing in many individuals but if the vcf is prepared correctly, it will work.
I am happy to help using it if necessary and the documentation is at: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
I use beagle4.1 for phasing diploid data from vcf files. It is very practical and easy to use on the command line.
I used Beagle to phasing genotypes considering windows of four SNPs with no overlapping with this command: java -jar beagle.r1399.jar gt=plink.vcf windows=4 overlap=0. Is it right? thanks in advance
David Kainer yes you can use plink to manipulate your vcf file (plink --vcf vcffile.vcf)
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