root@DESKTOP-1N42TVH:/home/test3# ls## 转换结果plink.hwe plink.log plink.nosex result.log result.map result.nosex result.pedresult.vcfroot@DESKTOP-1N42TVH:/home/test3# vcftools --vcf result.vcf --site-pi --outvcf_pi## 计算杂合度piVCFtools-0.1.16(C) Adam Auton and Anthony Marck...
–site-pi计算所有位点的多样性值 –window-pi, --window-pi-step计算窗口中的核酸多样性值 FST计算 –weir-fst-pop FILE:file must contain a list of individuals (one individual per line) from the VCF file that correspond to one population,可多次,生成weir.fst文件 –fst-window-size, --fst-windo...
6.在一系列位置输出核苷酸多样性 zcat input_file.vcf.gz|vcftools--vcf---site-pi--positions SNP_list.txt--outnucleotide_diversity
6.在一系列位置输出核苷酸多样性 zcat input_file.vcf.gz | vcftools --vcf - --site-pi --positions SNP_list.txt --outnucleotide_diversity AI代码助手复制代码
–site-pi 计算所有SNP –window-pi –window-pi-step FST计算 –weir-fst-pop<filename></filename> –fst-window-size –fst-window-step 其它计算 –het –hardy –site-quality 主要用于提取VCF文件中每个位点的QUAL信``` --missing-indv --missing-site 计算每个位点的缺失率 ...
–site-pi 计算所有SNP –window-pi –window-pi-step Measures the nucleotide diversity in windows, with the number provided as the window size. The output file has the suffix “.windowed.pi”. The latter is an optional argument used to specify the step size in between windows.滑动窗口计算slid...
--site-pi Measures nucleotide divergency on a per-site basis. The output file has the suffix ".sites.pi". --window-pi--window-pi-step Measures the nucleotide diversity in windows, with the number provided as the window size. The output file has the suffix ".windowed.pi". The latter is...
--window-pi ：指定窗口大小 --window-pi-step ： 指定步长大小 out.windowed.pi 4. vcftools去除...
1. 提取基因型信息：使用--extract-FORMAT-info选项，vcftools可以提取特定的基因型信息。2. 提取指定区域的变异信息：通过参数--vcf、--chr、--form-bp和--to-bp，用户可以指定一个区域，vcftools将提取该区域内的变异信息，输出到指定的文件中。3. 对vcf文件进行划窗处理：使用--window-pi和--...
site in the bcf file that does not have any missing genotypes vcftools --bcf input_file.bcf --hardy --max-missing 1.0 --out output_noMissing Output nucleotide diversity at a list of positions zcat input_file.vcf.gz | vcftools --vcf - --site-pi --positions SNP_list.txt --out ...