Open PollyRosy opened 2 months ago
I met the same error too, have you solved it?
I think it's version issue, when I use lower version everything goes well. @jiabowang Could you check this problem?
Instead of hapmap. I converted to ped and map using plink.
Instead of hapmap. I converted to ped and map using plink.
This is what I did too.
OK then. I think it would work when there only SNP exits because plink does not support INDEL, which I intend to keep in my GWAS analysis ;)
Hi all, I have fixed this error. Please try again with new GAPIT function.
Hi all, I have fixed this error. Please try again with new GAPIT function.
Where is the new GAPIT function? The file at https://zzlab.net/GAPIT/gapit_functions.txt says it's version 3.4.
The function in zzlab has not been updated. Please try this one.
The version is not changed. The current version is 3.4.
The function in zzlab has not been updated. Please try this one.
Hi, I used this script, but it still output the error:
Could you send me the genotype file?
Xiukun Yao @.***> 于2024年7月19日周五 22:54写道:
The function in zzlab has not been updated. Please try this one.
gapit_functions.txt https://github.com/user-attachments/files/16310042/gapit_functions.txt
Hi, I used this script, but it still output the error: image.png (view on web) https://github.com/user-attachments/assets/b1a0204d-068a-459f-8f5b-8f58b7cfac88
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Hello,
I update GAPIT version 3.4.0 and introduce the gapit_functions.txt. Hovewer I still have a problem.
[1] "--------------------- Welcome to GAPIT ----------------------------" [1] "MLM" [1] "--------------------Processing traits----------------------------------" [1] "Phenotype provided!" [1] "The 1 model in all." [1] "MLM" [1] "GAPIT.DP in process..." [1] "Converting genotype..." [1] "Converting HapMap format to numerical under model of Middle" [1] "Perform numericalization" Error in count.temp[, 2] : subscript out of bounds
Thank you Cecilia
@ceciliabruno Please check your HapMap file whether there are different symbols for missing genotype.
@ceciliabruno Please check your HapMap file whether there are different symbols for missing genotype.
Hello, Thank you for your answer. I reviewed the HapMap file and I solved the problem. Currently, I have another problem with " Manhattan plot (Genowise)...".
Thank you Cecilia
How many chromosomes are in your genotype file?
How many chromosomes are in your genotype file?
Hello,
There are 8 chromosomes in the genotype file. Thank you Cecilia
@ceciliabruno , Please check your genotype file or you can sent it with me. I can help with checking.
Hello. I encountered a very basic problem but I do not know how to fix it. I would appreciate it if you could help me. Thanks in advance. In my hapmap files, which converted from vcf, there are 2 nucleotide acids (bit=2?) and there are some multiallelic sites, but I removed them manually for now. I converted the vcf to Hapmap using the following way: https://github.com/wenkaiyan-kevin/vcf-to-hapmap.
I think there must be something wrong happening on data input?