Linkage data should be in the Linkage Pedigree (pre MAKEPED) format, with columns of family, individual, father, mother, gender, affected status and genotypes. The file should not have a header line (i.e. the first line should be for the first individual, not the names of the columns). Please note that Haploview can only interpret biallelic markers — markers with greater than two alleles (e.g. microsatellites) will not work correctly. A sample line from such a file might look something like:

3    12    8    9    1    2    1 2    3 3    0 0    4 2
a     b    c    d    e    f    -----------g------------ 

It is also worth noting that this format can be used with non-family based data. Simply use a dummy value for the pedigree name (1, 2, 3...) and fill in zeroes for father and mother ID. It is important that the "dummy" value for the ped name be unique for each individual. Affection status can be used to designate cases vs. controls (2 and 1, respectively).

Files should also follow the following guidelines:

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. This is the standard format of Genehunter's TDT output. See the sample below:

FAM1    FAM1M01    0    4    2    2
FAM1    FAM1M01    0    4    2    2
FAM1    FAM1F02    3    h    1    2
FAM1    FAM1F02    3    h    1    2

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. That is, if an individual is heterozygous at a locus, both alleles should be "h" if the phasing (which allele falls on which chromosome) is uncertain.

Data from the HapMap Project can be dumped by region using the GBrowse interface. The saved data file is in a marker-per-line format which can be loaded in Haploview.

GBrowse dumps only one file, which has one marker per line and which includes familial relationships among the HapMap samples as well as marker position information. The file format has several header lines (beginning with "#") which Haploview parses. Open the file by selecting "Browse HapMap Data" option and selecting the downloaded file.

If you wish to load data from another source in HapMap style format, you will need to specify pedigree information in the header of the file you've created. This can be done by creating lines of the following format at the top of your file:

#@ FAM01 NA0001 0 0 1 1

This data is the same as the pedfile format discussed above. That is, the fields are family,individual,father,mother,gender,affected status. You would then replace the NAXXXX identifiers in the header row of the HapMap file with your identifiers, subject to two important constraints: they must be unique across the entire dataset, not just within a family and they must begin with the characters NA.

Data in the HapMap PHASE format can be loaded into Haploview using three separate files. The first is the data file containing binary allele information. The second is a sample file containing a single column of the individual IDs used in the dataset. The third is a legend file containing four columns: marker, position, 0, and 1. Only the legend file requires a header and is used to decode the information in the data file. These files can be loaded in as GZIP compressed files using the "Files are GZIP compressed" checkbox on the initial loading screen. For more information on the HapMap PHASE format, please see the HapMap PHASE readme.

Data in the HapMap PHASE format can also be automatically downloaded into Haploview using the "HapMap Download" tab in the load screen by specifying the HapMap Release, chromosome, analysis panel, and start and end positions (in kb). These options can also be automatically filled in by querying the GeneCruiser database with a gene or SNP ID. More information about the GeneCruiser database can be found at the GeneCruiser website.

The marker info file is two columns, marker name and position. The positions can be either absolute chromosomal coordinates or relative positions. It might look something like this:

marker01 190299
marker02 190950
marker03 191287

An optional third column can be included in the info file to make additional notes for specific SNPs. SNPs with additional information are highlighted in green on the LD display. For instance, you could make note that the first SNP is a coding variant as follows:

marker01 190299 CODING_SNP
marker02 190950
marker03 191287

Output files from PLINK can be loaded into Haploview using the PLINK tab on the initial loading screen. PLINK files must contain a header and at least one column header must be titled "SNP" and contain the marker IDs for the results in the file. PLINK loading also requires a standard PLINK map or binary map file corresponding to the markers in the output file. The map file can be either three or four headerless columns (the Morgan distance column is optional). The map file can also be embedded in the results file as the first few columns of the file using the "Integrated Map Info" checkbox. You can load in non-SNP based files as well by checking the "Non-SNP" box. These files do not require a map file. You can choose to only load in one chromosome from your results file using the "Only load results from Chromosome" checkbox and selecting a chromosome from the dropdown list. You can also select which columns to load from your results file by checking the "Select Columns" checkbox. For a great deal more information on PLINK outputs, please see Shaun Purcell's PLINK website.

The "-batch" flag on the command line allows you to run Haploview automatically (in nogui mode) on several files. Batch input files should have one genotype file per line, along with an info file (if desired) separated by a space. Filenames must conform to the following rules:

The following example shows 2 pedfiles (with info files) and a hapmap file:

sample1.ped   sample1.info
sample2.ped   sample2.info
sample3.hmp

LD text output is a tab delimited set of columns containing the various measures of LD used by the program. Details for each column are shown below:

Details about additional options for this output type can be found below in the Export Options section.

When saving the LD table to a PNG, Haploview saves an image using the current display settings. This includes color scheme, zoom and proportional spacing. Thus, in order to save a less detailed image to a PNG, first zoom out, then export the tab. Note that Haploview cannot save large datasets at the higher zoom levels. For more information see the Export Options section below.

Haplotype output shows a block, its markers, the haplotypes and their population frequencies, the crossover percentages to the next block and the multiallelic D prime. Crossover percentages are shown as a matrix with this block's haplotypes as the rows and the next block'shaplotypes as the columns. An example might look like:

BLOCK 1.  MARKERS: 1 2 3 4
3312 (0.825)    |0.800  0.025   0.000|
1144 (0.163)    |0.031  0.125   0.007|
3342 (0.013)    |0.006  0.000   0.006|
Multiallelic Dprime: 0.802
BLOCK 2.  MARKERS: 10 11 12
441 (0.837)
222 (0.150)
242 (0.013)

In this example, the first block has 4 markers with 3 haplotypes displayed and the second block has 3 markers and 3 haplotypes. The tag SNPs for each block are (3,4) and (10,11) respectively. The crossover percentage matrix can be read as follows: 80% of all samples have the pattern 3312-441, 3.1% have the pattern 1144-441 and so forth.

Saving the haplotype tab to a PNG produces an image using the current display settings (such as haplotype frequency cutoff).

Single marker association results are saved in a tab-delimited text file with the following columns:

Trio (TDT) data only:

Case-Control data only:

Haplotype association text output is a tab-delimited file, broken into sections by block. The columns are:

Trio (TDT) data only:

Case-Control data only:

The output from the permutations tab shwos the number of permutations performed and then a tab-delimited table with one row per permuted test and the following columns:

The Tagger text output begins with several pieces of summary information. More details on this can be found in the Tagger section. The rest of the output is divided into two sections. The first lists each marker, with the following rows:

The second part consists of a list of the tests and the alleles they capture best.

This file is the same format used by Haploview for custom association tests and exported by Tagger. It is discussed below in the auxiliary files section.

This file is the same format used by Haploview for custom association tests and exported by Tagger. It is discussed below in the auxiliary files section.

The marker check data is a tab-delimited file with the following columns:

The PLINK text output is a tab-delimited file of the current view of the data in the PLINK tab. Please note that while the filtering state is preserved in this output, the sorting state is not.

The default setting (and only one available for most tabs) is to use all the markers.

Generates the LD text or PNG file for only a specific range of markers.

Generates the LD text file for only adjacent markers. This can be useful to view the T-int stat, which measures LD information content in the gaps between markers.

You can specify a set of blocks by loading a blocks file. Each line is a space separated list of markers with one block per line. For example:

1 2 3 4
9 10 11 12 13 14 15

Would create one block from markers 1-4 and another from 9-15. The first marker in the file is number 1 (not 0).

You can add an analysis track along the top of the LD display by loading a file with two columns, <position> <value>. Haploview will plot the values continuously with respect to the positions of the markers, so the positions should use the same coordinates as the marker info file. For example:

1000 0.3
2000 1.7
3000 11.0
4000 2.3
5000 4.6

Would plot a line from position 1000 to 5000. The values can be of any units or magnitude, as the Haploview scales the analysis track to the bounds of the values.

You can specify a set of custom association tests for Haploview to perform. The format takes both single marker tests and multi-marker tests (which require you to specify alleles for those markers). The format is one test per line with each line containing one of the following: a single marker name or several comma separated names, then a tab, then comma separated alleles for each marker. This format is exported by Haploview using the "Dump Tests" button in the Tagger Results panel and by Paul deBakker's Tagger webpage.

For instance, the following example would create 5 tests: markers 1, 2 and 3 individually, all the alleles (haplotypes) of the block 4,5,6 and the CAA haplotype of the block 12,13,14:

marker1
marker2
marker3
marker12,marker13,marker14     2,1,1

N.B. Using a Custom Association Tests File requires a marker info file, since the tests file reads the marker names as specified in the info file.

You can specifiy a list of markers for Tagger to include or exclude from those markers available for selection as tag SNPs. In either case the format is the same: one marker name per line. The following file could be used to either include or exclude markers 1,7 and 9:

marker1
marker7
marker9

N.B. Using a Tagger Include/Exclude File requires a marker info file, since it reads the marker names as specified in the info file.