IBDLD Activity
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Activity for IBDLD
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Lide Han posted a comment on a wiki page
I am sorry for late response. You can use -chr to set specific chromosomes for the analysis Lide Han
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BRT posted a comment on a wiki page
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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Fernando Silva Aguilar posted a comment on a wiki page
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,...
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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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IBDLD released /Version History.doc
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Peicheng Jing posted a comment on a wiki page
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...
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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.
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If you meet some problems, please let me know. Welcome provide some advice.
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