在用EMMAX做关联分析时,#kinship 亲缘关系矩阵计算 ibs-kinship emmax-kin-intel64 -v -s -d 10 -o ./pop.kinship.IBS snp_var 用这条命令计算亲缘关系,得到的pop.kinship.IBS全是NA

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马杰宇

root@77146ac2bf18  21:42:19 /work/my_gwas/09.gwas_emmax]# emmax-kin-intel64 -v -d 10 -o ./pop.kinship.BN snp_var


Reading TFAM file snp_var.tfam ....

Memory allocated, nrows = 258, nheadercols = 6, nvaluecols = 0

Freeing cmat

Freeing cheaders

Memory freed

Identified 258 individuals from TFAM file

Setting # unit lines = 1937726 to fit the memory requirement

Reading TPED file snp_var.tped ....

Reading 0 SNPs

Reading 10000 SNPs

Reading 20000 SNPs

Reading 30000 SNPs

Reading 40000 SNPs

Reading 50000 SNPs

Reading 60000 SNPs

Reading 70000 SNPs

Reading 80000 SNPs

Reading 90000 SNPs

Reading 100000 SNPs

Succesfully finished reading TPED file

Printing the kinship matrix to file snp_var.

可以成功输出,但是都是na

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omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

这个需要测试,检查输入文件是否有问题;

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  • 马杰宇 提出于 2024-01-18 22:21