Haploview formats
1
0
Entering edit mode
12 days ago

Hello, How can I create a standard linkage format file as an input for Haploview or convert my excel sheet to this format or other acceptable input formats?

Haplotype Analysis • 227 views
ADD COMMENT
0
Entering edit mode
12 days ago

Input file formats are elaborated here: https://www.broadinstitute.org/haploview/input-file-formats

My recommendation to you is to get your data converted into PLINK format, from where you can perform many standard analyses, and also convert this further to many other formats (including Haploview).

As you have not explained in detail what data you currently have, there's no specific help that can be offered.

Kevin

ADD COMMENT
0
Entering edit mode

Many Thanks Kevin. I am undergoing a case-control study that tried to find the association between two SNPs on the same gene with Ischemic Stroke(IS). And I had the statistical analysis made by a statistician. The results showed the association of only one SNP with IS. The reviewers asked me to check the possibility that the two SNPs constitute a haplotype. As I am new in this field and I have my raw data in .xlsx format, I've searched for programs to perform this and I have already installed Haploview and Tassel. I have already reached the link you sent above and knew the formats requested by haploview but still have a problem in the know-how. On my search journey, up till now I've succeeded only in converting the excel file into (.hmp.text) format and could open this into tassel. I am asking now for your further recommendation

ADD REPLY
0
Entering edit mode

I see, sounds quite interesting. If you can already get the data into Tassel, then all that you need to do is perform Linkage Disequilibrium (LD) - variants with high LD may be part of the same haploblock. It really is as simple as that, in this case, as a reply to a reviewer. You can search publications to find out which cut-off to use for LD, but Tassel probably already has a default value.

For what it is worth, and for others arriving here, I have some code to identify haploblocks, but coming via the VCF/BCF + PLINK + HaploView route, here: How do I compute ld blocks from the hapmap ld_data?

ADD REPLY
0
Entering edit mode

This seems pretty helpful. Thank you so much.

ADD REPLY

Login before adding your answer.

Traffic: 2239 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6