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2018-07-21 09:47 阅读 4.7k

请问plink对VCF格式的数据进行格式转化时,会出现文件后缀为hh,nof和nosex文件呢

10

我按照以下流程进行主成分分析:
1、利用vcftools软件进行格式转换:vcftools --vcf tmp.vcf --plink --out tmp
--plink, 改变输出文件格式
此时会生成两个文件:tmp.ped(基因型数据) 和 tmp.map
2、利用plink软件进行数据格式转换:./plink --noweb --file tmp --make-bed --out tmp
注意,输入文件和输出文件都不需要文件名的后缀,此时生成3个文件:tmp.bed,tmp.bim 和 tmp.fam 
3、利用gcta软件进行pca构建
gcta --bfile tmp --make-grm --autosome --out tmp
此时生成一个文件:tmp.grm.gz

但是在使用plink对VCF格式的数据进行格式转化时,会出现文件后缀为hh,nof和nosex文件图片说明
在接下来利用gcta软件进行pca构建时,出现了以下错误:
Skipping web check... [ --noweb ]
Writing this text to log file [ sample_210JS.fltsnp.log ]
Analysis started: Tue Jul 10 09:21:15 2018

Options in effect:
--noweb
--file /lustre/waterfowl_group/practice/geneic_evolution/data/ped_map/sample_210JS.fltsnp
--make-bed
--out sample_210JS.fltsnp

** For gPLINK compatibility, do not use '.' in --out **
54599752 (of 54599752) markers to be included from [ /lustre/waterfowl_group/practice/geneic_evolution/data/ped_map/sample_210JS.fltsnp.map ]
Warning, found 210 individuals with ambiguous sex codes
Writing list of these individuals to [ sample_210JS.fltsnp.nosex ]
210 individuals read from [ /lustre/waterfowl_group/practice/geneic_evolution/data/ped_map/sample_210JS.fltsnp.ped ]
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 210 missing
0 males, 0 females, and 210 of unspecified sex
Before frequency and genotyping pruning, there are 54599752 SNPs
210 founders and 0 non-founders found
697384 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ sample_210JS.fltsnp.hh ]
15 SNPs with no founder genotypes observed
Warning, MAF set to 0 for these SNPs (see --nonfounders)
Writing list of these SNPs to [ sample_210JS.fltsnp.nof ]
Total genotyping rate in remaining individuals is nan

请问这是哪里出了问题呢?望大神解答

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1条回答 默认 最新

  • benson2007benson benson2007benson 2018-07-21 09:56

    将 impute 之后的文件转化为 tped 的 plink 格式!

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