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bioinformatics-ptp / Zanardi

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Specify different chip in FImpute #3

Open JulieIgX opened 7 years ago

JulieIgX commented 7 years ago

Dear all,

I have a question regarding the use of FImpute into Zanardi. Is it possible to specify different chip ? When we run FImpute apart from Zanardi we can put different "chip number" in the genotype file and specify "order of SNP for each chip" in the snp_info_file. How can we do that with Zanardi? If it's not possible, did you decide to not include this possibility because it 's not very useful to specify chip?

Thanks in advance for your help Regards Julie

malbianco commented 7 years ago

Hi Julie

I checked your question carefully before answering you. At the moment, Zanardi creates a specific file for Fimpute. This file always contains number 1 in the "chip" column. So, if you introduce "Chip Number" in the paramfile.txt maybe he does not do what you want. Including the chip number in the program is difficult. Perhaps it would be possible to do it if the files were merged into Zanardi, but if you have, for example, hd and 50k already in one file, Zanardi can not recognize which chip is which animal. I think it's difficult even if it's Zanardi to make the merge. Because you can have two 50K files with a number of different SNPs (eg one with 53,000 SNPs and the other with 43,000 SNPs). Let me know if I have not been clear

Regards, Gabriele

JulieIgX commented 7 years ago

Hi Gabriele, Thank you for your answer. I understand the difficulty to include the chip number in the program but anyway I'm not sure that this information is really important for the program. I will do some comparison with and without the chip number to be sure. Regards, Julie