I have genome sequences for 14 unrelated wild mouse samples. I'd like to use GIBDLD to scan for selective signitures because it looks to me it's a very powerful method. I tried to run on chromosome 10 which has over 700,000 SNPs, I used -hiddenstates = 3 and -ibd = 3. Out of 105 pairs, I got identity coefficient = '-nan' for all SNPs for 51 pairs when I used unphased data, while I got '-nan' for 43 pairs when I used phased data (Inferred by Beagle). Those pairs are random and didn't invlove any particular individuals. I tried to run those pairs separately and I still got '-nan'. There's no error message, and I couldn't figure out what went wrong.
Could you give me any suggestions? Thank you very much.
Peicheng
Programmer Analyst
UW-Madison
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Peicheng,
The problem may come from map file. For IBDLD, it requires the SNPs have been arranged from smallest to largest across chromosome in map file. If the SNPs are not sorted, '-nan' will be obtained.
Lide Han
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I have been running IBDLD program for a set of 50 inbred lines of maize. I have been using GIBDLD program which gave me good results. However, recently I found some pedigree information about each inbred line and I am trying to run LD-RR method. I have in total 160158 SNP across 10 chromosomes. The chromosome 1 have 24846 markers. I run method LD-RR with -ploci 10 -dist 2, the kinship file created using IdCoefs 2.1.1, and with hidden states 90. When looking at the results from ibdtxt file, I am having some pair of individuals with probability coded as "nan" for some chromosomes but not for others. I sorted the map file based on the physical position (basepairs) and genetic position (cM) and still have the same result. There's no error message, and I couldn't figure out what went wrong.
Could you please give any sggestion on how to solve this?
Thanks in advance for all your help.
Sincerely,
Fernando Silva Aguilar
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Dr. Han,
is there any way to make IBDLD to use specific chromosomes in the analysis. For example if I want to use chromosomes 1 to 5. Currently I can specify to use one chromosome.
Thanks,
BRT
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If you meet some problems, please let me know.
Welcome provide some advice.
IBDLDv3.38 is the version which obtain the most accurate IBD estimate in comparison with all previous ones.I hope many more users can use it.
Dr. Han:
I have genome sequences for 14 unrelated wild mouse samples. I'd like to use GIBDLD to scan for selective signitures because it looks to me it's a very powerful method. I tried to run on chromosome 10 which has over 700,000 SNPs, I used -hiddenstates = 3 and -ibd = 3. Out of 105 pairs, I got identity coefficient = '-nan' for all SNPs for 51 pairs when I used unphased data, while I got '-nan' for 43 pairs when I used phased data (Inferred by Beagle). Those pairs are random and didn't invlove any particular individuals. I tried to run those pairs separately and I still got '-nan'. There's no error message, and I couldn't figure out what went wrong.
Could you give me any suggestions? Thank you very much.
Peicheng
Programmer Analyst
UW-Madison
Peicheng,
The problem may come from map file. For IBDLD, it requires the SNPs have been arranged from smallest to largest across chromosome in map file. If the SNPs are not sorted, '-nan' will be obtained.
Lide Han
Dr. Han:
I have been running IBDLD program for a set of 50 inbred lines of maize. I have been using GIBDLD program which gave me good results. However, recently I found some pedigree information about each inbred line and I am trying to run LD-RR method. I have in total 160158 SNP across 10 chromosomes. The chromosome 1 have 24846 markers. I run method LD-RR with -ploci 10 -dist 2, the kinship file created using IdCoefs 2.1.1, and with hidden states 90. When looking at the results from ibdtxt file, I am having some pair of individuals with probability coded as "nan" for some chromosomes but not for others. I sorted the map file based on the physical position (basepairs) and genetic position (cM) and still have the same result. There's no error message, and I couldn't figure out what went wrong.
Could you please give any sggestion on how to solve this?
Thanks in advance for all your help.
Sincerely,
Fernando Silva Aguilar
Dr. Han,
is there any way to make IBDLD to use specific chromosomes in the analysis. For example if I want to use chromosomes 1 to 5. Currently I can specify to use one chromosome.
Thanks,
BRT
I am sorry for late response. You can use -chr to set specific chromosomes for the analysis
Lide Han