Haploview Throws Out "Force To Includ" Snp

Question

[sci11168]

Hi there:

Just wonder if anyone came across the same problem in Haploview before.

I’m trying to use Tagger in Haploview in command mode (Windows) to test if my collection of SNP would work as tag SNP. Therefore, I’ve tried to scan for tag SNP on each chromosome and force include SNPs from my collection on that chromosome. The SNP list is one rsNo per line in windows. However, tagger throws out my SNPs by saying something like:

Warning: skipping marker rs12565115 in the list of forced included tags since I don't know about it.

Warning: skipping marker in the list of forced included tags since I don't know about it.

It always begin with a line showing the rsNo and then a line with No rsNo.

May I know if that’s because something wrong with line terminator in windows?

[zx8754]

I am getting same warning, did you manage to solve this?

Answer 1

[zx8754]

From Tagger FAQ:

What are include tag SNPs? You can force in sets of SNPs by submitting a file containing SNP identifiers, or pasting this in the textbox. Tagger will then take this into account when picking new tag SNPs. Useful if you already have genotype data for some SNPs but want to pick extra tag SNPs. Or if you want to include some SNPs that have been previously shown to be associated. Make sure that the SNP identifiers are exactly the same (case-sensitive!) as those in the .info file

In your case it might be that force include list SNPs are not in your info file. I had similar warning message, but it was because I used wrong option to force include, used -includeTags instead of -includeTagsFile

From Manual:

-includeTags <markers> Forces in a comma separated list of marker names as tags.
-includeTagsFile <file> Forces in a file (or http:// location) of one marker name per line as tags.