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Hi!
I'm hoping someone has encountered my problem before! I am working with Illumina HD canine array data. I am trying to get LD data and make LD decay plots. What I want is to load single chromosomes into Haploview and get the output LD text files. However Haploview doesn't like to load my files and I get error messages. I have successfully made Haploview ready files through Gpliink and they open fine in Haploview (.info and .ped) - however when I load them through gPlink the option to change the size of the pairwise comparisons does not exist (i.e. it is limited to 500 kb) and I want to force all pairwise comparisons. The load data window in haploview does not accept my traditional map and ped files because they are coded for dog chromosomes (i.e. too many).
Because I am working with dog samples - the drop downs to limit CHR number are also not useful in gPlink/Haploview. I have made snp lists to use for limiting my files (because Haploview on my system ) will not handle doing all 170k markers at once as I run out of memory. Using these list files I have generated recodedHV files in gplink (filtered for snps on a single chromosome at a time). The output files are .ped, .info, .log, etc
also - I know how to force more memory in my command line - however since I have been having to load the files by right clicking in g plink - I don't get to insert the use more memory command in haploview.
Any help is greatly appreciated and I can provide more details where needed!
Thanks!
Josh
I'm hoping someone has encountered my problem before! I am working with Illumina HD canine array data. I am trying to get LD data and make LD decay plots. What I want is to load single chromosomes into Haploview and get the output LD text files. However Haploview doesn't like to load my files and I get error messages. I have successfully made Haploview ready files through Gpliink and they open fine in Haploview (.info and .ped) - however when I load them through gPlink the option to change the size of the pairwise comparisons does not exist (i.e. it is limited to 500 kb) and I want to force all pairwise comparisons. The load data window in haploview does not accept my traditional map and ped files because they are coded for dog chromosomes (i.e. too many).
Because I am working with dog samples - the drop downs to limit CHR number are also not useful in gPlink/Haploview. I have made snp lists to use for limiting my files (because Haploview on my system ) will not handle doing all 170k markers at once as I run out of memory. Using these list files I have generated recodedHV files in gplink (filtered for snps on a single chromosome at a time). The output files are .ped, .info, .log, etc
also - I know how to force more memory in my command line - however since I have been having to load the files by right clicking in g plink - I don't get to insert the use more memory command in haploview.
Any help is greatly appreciated and I can provide more details where needed!
Thanks!
Josh