Hi can any one recommend any software for working with phased VCF files?
I've a complete 4 generation pedigree (Grandparents, Parents, Proband, Children) which I've phased using a couple of methods (GATK PhaseByTransmission, RTG Pedigree Phasing, Beagle4) and I'm looking for a good way to visualize the flow of genotypes/haplotypes through the pedigree.
Programs that take in other formats would be welcome as well (assuming it's not too hard to convert VCF to their format).
Otherwise looks like I'll need to do some coding...
Thanks!
1 answer
A colleague of mine developed a tool called jenti that is intended for kinship calculation, but is also useful for plotting pedigrees. I strongly recommend it. You can give a look at www.jenti.org. The reference is the following:
Jenti: an efficient tool for mining complex inbred genealogies. Mario Falchi and Christian Fuchsberger Bioinformatics 2008 24: 724-726.
An additional free software package that can plot pedigree (and also some plot of haplotypes, if I well remember) is genehunter, a package for linkage analysis.
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