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From: Mao J. <jia...@gm...> - 2011-06-09 21:07:59
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Dear VCFtools-helpers, I have benefit much from your kind helps and directions. Thanks a lot. Here, I still want to get much more from you. This problem is not from any errors/bugs of VCFtools. I just want to take advantage of the excellent functionalities of VCFtools. I want to learn how to use the more complex (for me) part of it. I want to estimate the decay of LD, by resampling a starting point 10,000 times on a chromosome (here chromosome 1) for all the individuals in a VCF file (mydata.vcf.gz). My data are haplotypic data (phased). The pariwise haplotypic r2 need to be calculated for every pair of SNPs within 25-kb of this starting point. I read the online guide for: - --hap-r2 - --geno-r2 - --ld-window <int> - --ld-window-bp <int> - --min-r2 <float> But, I am not clear how to do my this job. Could you please give my any directions on this problem? Thanks in advance. Best, Jian-Feng, Mao ########################################################## Here possible lines of command, please correct me. # for this command, I do not know how to resampling a starting point 10,000 times on a chromosome vcftools --vcf mydata.vcf.gz --chr 1 --hap-r2 ld-window 25000 --out mydata.ld |