Output File Formats

Output Files

For any given tab the information in the display can be saved. For the data check and association test tabs, a simple tab-delimited text file is generated from the tables. For the LD and Haplotype tabs, data can either be dumped to text files or the image can be saved to a PNG.

LD Text Output File

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:

• L1 and L2 are the two loci in question, referenced by their number or name (if marker info file is provided)
• D' is the value of D prime between the two loci.
• LOD is the log of the likelihood odds ratio, a measure of confidence in the value of D'
• r2 is the correlation coefficient between the two loci
• CIlow is 95% confidence lower bound on D'
• CIhi is the 95% confidence upper bound on D'
• Dist is the distance (in bases) between the loci, and is only displayed if a marker info file has been loaded
• T-int is a statistic used by the HapMap Project to measure the completeness of information represented by a set of markers in a region

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

LD PNG Output

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 Text Output File

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.

Haplotype PNG Output

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

Single Marker Association Text Output File

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

• # is the marker number.
• Name is the marker ID specified if an info file is loaded.
• Chi Square is the chi square value for the marker.
• p value is the significance level for the above chi square.

Trio (TDT) data only:

• Overtransmitted is the allele overtransmitted to affected offspring.
• T:U is the ratio of transmissions to non transmissions of the overtransmitted allele (see above).

Case-Control data only:

Case-Control data only:

• Case Control Ratios are the ratios (shown as either counts or quotients, depending on selected options) for the case and control populations, respectively.

Permutation Text Output File

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:

• Name is the test name, which is either a marker name or a comma separated list of marker names then a tab then a comma separated set of alleles for those markers.
• Chi Square is the observed association chi square for that test.
• Permutation p-value shows the significance of the test among the permutation tests.

Tagger Text Output File

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:

• Marker is the marker name.
• Best Test is the test with the highest r² to this marker.
• r2 w/test is the r² between this marker and its test.

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

Tagger Tests Dump

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.

Tagger Tags Dump

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.

Marker Check Text Output File

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

• # is the marker number.
• Name is the marker ID specified (only if an info file is loaded).
• Position is the marker position specified (only if an info file is loaded).
• ObsHET is the marker's observed heterozygosity.
• PredHET is the marker's predicted heterozygosity (i.e. 2*MAF*(1-MAF)).
• HWpval is the Hardy-Weinberg equilibrium p value, which is the probability that its deviation from H-W equilibrium could be explained by chance.
• %Geno is the percentage of non-missing genotypes for this marker.
• FamTrio is the number of fully genotyped family trios for this marker (0 for datasets with unrelated individuals).
• MendErr is the number of observed Mendelian inheritance errors (0 for datasets with unrelated individuals).
• MAF is the minor allele frequency (using founders only) for this marker.
• Alleles are the major and minor alleles for this marker.
• Rating is "BAD" if the marker failed any of the above tests and blank otherwise.

PLINK Table Text Output File

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.