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
andL2
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 ofD'
-
r2
is the correlation coefficient between the two loci -
CIlow
is 95% confidence lower bound onD'
-
CIhi
is the 95% confidence upper bound onD'
-
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:
-
Major Alleles
are the major alleles in the case and control populations respectively. -
Case Control Ratios
are the ratios (shown as either counts or quotients, depending on
selected options) for the case and control populations, respectively.
Haplotype Association Text Output
Haplotype association text output is a tab-delimited file, broken into sections by block. The columns are:
-
Haplotype
is the sequence of alleles for this haplotype in this block. -
Frequency
is the population frequency for this haplotype. -
Chi Square
is the chi square value for the haplotype. -
p value
is the significance level for the above chi square.
Trio (TDT) data only:
-
T:U
is the ratio of transmissions to non transmissions of the haplotype to affected offspring.
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.