I am currently trying to run LD analysis on Haploview, using a .ped file from the Drosophila Genetic Reference Panel, which includes indels. It looks like this is causing an error in the analysis. Is there any way to remove these from the .ped file or get Haploview to accept them?
You're right, Haploview doesn't accept indels encoded in the .ped file. You can easily remove indels with plink using the --snps-only command. Alternatively you may be able to encode the indel differently using the plink --recode 12 command, which encodes the ref allele as 1 and alt allele as 2. However, please note that you will lose information using this method (i.e. you will not know the specific nucleotides of the ref and alt alleles and I think haploview assumes 1=A and 2=C, therefore this is how the data are displayed in Haploview). Hope that helps.
Dear Teresa,
I'd like to add something to Amy's good answer:
Imagine you have an AG to G deletion and a T toTC insertion.
To remember which allele is which, you may change AG to A and TC to C. So:
Open your -ped file in Excel
Do find replace to recode these indels according to above.
Save as .csv
Open in text editor and find replace the commas with tab. Save and close.
This file is now readable by Haploview.
Even if you have a couple of these, it is worth doing this to keep the indels.
Hope it helps.
Thank you Amy and Naser for the answers =) but I still get errors in the analysis.
I am using Haploview as an add-in in Excel, may I know where do I find plink --recode 12 command?
Naser,
Can you please elaborate more on the steps?
I did as you said:
1) my data is in Excel file, for the AG to G deletion, I labelled it as A and run haploview in Excel
2) then I open the .ped file in Excel and the data are all in numbers, the deletion is labelled as 1 0
3) i saved the file as .csv
4) opened it using Notepad
this is where I am lost... Am I suppose to replace all commas with tabs?
After saving this Notepad file, do I run Haploview again or just open the .ped file?
Please advise, thank you!!!
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