Question: how can I make input file for Haploview from Output files of inferred haplotypes by fastPHASE?
gravatar for mary
6.7 years ago by
Bologna university
mary210 wrote:

Dear all

I am doing LD analysis and selection signature on 50k snp data of cattle. For the analyses, fully phased haplotype data were required. After filtering process, I reconstructed haplotypes for every chromosome using default parameters in fastPHASE (Scheet & Stephens 2006).( Reconstructed haplotypes should be inserted intoHAPLOVIEWv4.1 (Barrettet al.2005) to estimate LD statistics based on pairwise r2). fastPASE Output files for inferred haplotypes or imputed genotypes contain two lines per given diploid individual, with the order of individuals corresponding to that supplied in the input file. and also, summary information is given, such as a recapitulation of some of the parameters from the fastPHASE run, and the command line supplied by the user.same as below










Haploview currently accepts input data in five formats, standard linkage format, completely or partially phased haplotypes, HapMap Projectdata dumps, PHASE format, and PLINK outputs.

the problem is that I don't know how can I make completely phased haplotypes from my output file of fastPASE to haploview input file. It should have below format:

FAM1     FAM1M01     0     4    2    2

FAM1     FAM1M01     0     4     2    2

FAM1     FAM1F02      3     h     1    2

FAM1     FAM1F02      3     h     1    2

Haplotype data for Haploview's input must be formatted in columns of Family, Individual and Genotypes. There should be two lines (chromosomes) for each individual.The data format uses the numerals 1-4 to represent genotypes, the
number zero to represent missing data, and the letter "h" to represent a heterozygous allele.

is there anyone that know any software or documentation to convert my data. forgive me if my question is basic.


ADD COMMENTlink modified 6.6 years ago by Biostar ♦♦ 20 • written 6.7 years ago by mary210

Have you got the answer of this question? As, I am doing same thing and also want to draw a NJ tree based on the fastPHASE inferred haplotypes.



ADD REPLYlink written 6.5 years ago by kumar.vinod81280

Hi Kumar

Unfortunately I still have problem with making input file of Haploview. I think I have to make Legen file format, but i dont know how?

ADD REPLYlink written 6.5 years ago by mary210

I am attaching a paper, I think match with our work, if you extract some information from there.

"Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication"


ADD REPLYlink written 6.5 years ago by kumar.vinod81280

Hi mary I have the same problem, if you have figured it out, could you teach me how to do it thanks John

ADD REPLYlink written 4.4 years ago by yanjuncong0
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