Hello,
What are some of the best software packages and viewers to examine haplotypes for a few specified chromosomes? Would IGV be appropriate? Generally are the input formats raw sequence files or can they be vcf files? I am trying to correlate this with ancestry.
One of the most common viewers is called HaploView. The publication has almost 12,000 citations: Haploview: analysis and visualization of LD and haplotype maps.
If you can get your data into PLINK format, then you can export to HaploView.
I am not aware of anything that allows you to view these genome-wide, but you may consider a customised solution via a chromosome karyotype plot: Creating chromosome karyotype plot with R and ggplot2
Thank you for your reply! I have changed my original post from "all chromosomes" to only a specific few. Also, I have tried HaploView without success and Broad no longer supports the package. I think the genome viewers (i.e. IGV and UCSC genome viewer) might be useful?
Well, they are general purpose viewers. The benefit of HaploView is that it shows nice figures. If you have data in BED, BAM, BigWig, GTF, etc., you can upload Custom Tracks to the UCSC Genome Browser.
In which format is your data?
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