Auxiliary Input Files

Auxiliary Input Files

Blocks File

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).

Analysis Track File

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.

Custom Association Tests File

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:

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.

Tagger Marker Include/Exclude 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:


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.