Question: Pedigree - Haplotype building and VCF files
gravatar for cadunesp
20 months ago by
United States
cadunesp0 wrote:

Hello everyone! I'm a beginner in bioinformatics, but I would like to know which program (s) I should use to building a haplotype family using vcf files and if there is some good program to visualize the results. I really appreciate your help! Carlos

next-gen • 713 views
ADD COMMENTlink modified 20 months ago by Kevin Blighe56k • written 20 months ago by cadunesp0
gravatar for Kevin Blighe
20 months ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

First, convert your VCF data into PLINK format (look up the PLINK documentation). If you have a single VCF of all samples, then I recommend splitting it into the different groups within each of which you want to identify haploblocks, and then creating separate datasets for these.

Within PLINK, you can do things like identifying 'tag' SNPs and calculate linkage disequilibrium, amongst other things. However, I recommend exporting your data from PLINK for input to HaploView with the following command:

plink --noweb --bfile MyPlinkDataset --chr 5 --from-bp 1000 --to-bp 100000 --snps-only no-DI --recodeHV --out MyPlinkDataset.Haploview ;

Within Haploview, you can run the popular program 'Tagger' (identifies tag SNPs), and also identify Haploblocks and their individual types (sequences that make up the haploblocks):




ADD COMMENTlink written 20 months ago by Kevin Blighe56k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1166 users visited in the last hour