Here is the Haploview input format explanation page:

http://www.broadinstitute.org/science/programs/medical-and-population-genetics/haploview/input-file-formats-0

The LINKAGE format is the traditional format used by Haploview, and that page goes into a fair amount of detail about that format. You have file input lines arranged with one line per individual. The first six columns describe the individual (FamilyID, IndividualID, Father, Mother, Sex, Affectation status), and the remaining columns are used for genotypes -- two columns per marker, one for each chromosome. Haploview also needs a marker information file so that it knows what to call the markers and where they lie on the chromosome. This is a two-column file with the first column the marker name (in the same order as columns in the LINKAGE file) and the second column the position on the chromosome (usually in base pairs).

If you have input lines arranged one line per genotype, with columns for each individual, it may be easier to process them through PLINK to convert to the one-line-per-individual LINKAGE format. Details on the PLINK "transposed" format, and how to convert to standard LINKAGE format can be found here:

http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr

I am quite familiar with these file formats (among others), and have a reasonable understanding of how Haploview works, so feel free to ask me any questions you have regarding recoding your data.

Haplostats package in R does a good job. Try it.

i have this file as an output for Affy.6.0 , i want to do LD for these list of SNP in Haploview i have used snp_tools to convert it >PLINK format but it does not work in haploview can you help please

Try the "Pairwise LD" feature in SNAP (http://www.broadinstitute.org/mpg/snap/ldsearchpw.php)

Thank you All. Haploview id great!

Dear David Eccles,

Could you please explain what are the numbers in the blocks of Haploview plot?

Haploview has many numbers, and saying "blocks" when you're talking about LD is doubly confusing. The numbers in the diamonds are D' values (one common measure of LD) in percent (!), with red and no numbers representing a D' value of 1 [assuming the standard graphical display]. Each haplotype block is enclosed by a dark/thick line, and there is a length statistic associated with that block. Numbers at the top between two adjacent blocks are the marker number based on the order of markers in the file, and don't have any particular relevance to the interpretation of the LD plot.

FWIW, I think it's wonderful that there are people who are still interested in haplotypes and LD. People were starting to discover really interesting stuff about the underlying nature of haplotype blocks (e.g. holes, overlapping blocks) before it all got swamped out by GWAS and NGS.

Thank you Dr. David Eccles. Can we analyze only 12 SNPs in a specific genomic region for associations with a specific disease? If yes, what program will be best? Being a bioinformatician, could you collaborate with us for these type of analyses in future. Thank you.

With 12 SNPs you can do pretty much anything, so my fall-back is a basic chi^2 test in R. However if the region is small enough (less than 1MB) you should probably do an LD analysis to look for evidence of haplotype blocks, and do a separate association test for the observed haplotypes within each block.

I'm happy to collaborate with you. You can contact me by regular email , or see www.gringene.org for more contact details.

Dear David,

I am so happy to find this conversation about the LD and Haploview! I am actually working on Pairwise LD measures for multiple SNPs and want to create a LD plot with Haploview. To do that, I used Plink to get a Plink output file to import into Haploview. Once I computed the LD measures for multiple SNPs with Plink (the command: --r2) I've got the following columns: CHR_A, BP_A, SNP_A,CHR_B, BP_B, SNP_B,R2. I'm not able to import this PLINK output into Haploview as any output file from PLINK must contain a SNP column to be loaded into Haploview. My question is How could I get a LD output using Plink with the SNP column required by Haploview?

Thanks for that.

Cheers,

Natacha

can you tell me what that fig. means? iam new in this area and need help 

Good morning.

I have to assess haplotypes frequency and linkage disequilibrium between 4 SNPs of the VEGFA gene. I have a typical excel database with an individual for each line. I tried to use snps tools in excel but after converting the file I cannot open it by haploview?

Can you help me in some way?

Each of you can also contact me by e-mail ([email protected]).

Regards

Dear Vincenzo,

I read your comments right now! 

If your problem still exist you may message me and discuss with more details.

Hamid

one can use the LDlink, it is a suite (at the following link) to do linkage disequilibrium test which provides various purpose-specific modules

https://ldlink.nci.nih.gov/?tab=home