# --window-pi-step,可选参数 L_donovani_all_samples_10kb.windowed.pi(不添加步长结果文件) 加入步长100b(--window-pi-step 100) 7,计算(Fst) vcftools --vcf L_donovani_all_samples.vcf --weir-fst-pop population1 --weir-fst-pop population2 --fst-window-size 10000 --out pop1_vs_pop2_F...
3. vcftools对vcf文件进行划窗处理 对vcf文件进行滑窗处理,统计每个自定义大小窗口内的变异位点数量和多态性pi值。 # 对上述提取的sample.recode.vcf进行处理vcftools --vcf sample.recode.vcf\--window-pi100--window-pi-step5# 结果文件# out.windowed.pi 参数说明: --window-pi :指定窗口大小 --window-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 an optional argument used to specify the step size in between windows.滑动窗口计算sliding windows,参考A refere...
–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-window-step FSTc滑动窗口计算,重测序一...
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--window-pi-step参数，用户可以对vcf文件进行滑窗处理，统计每个自定义大小窗口内的变异位点...
计算窗口的多态性(滑窗参数为可选项); vcftools --vcf test.vcf --window-pi <integer> --window-pi-step <integer> --out out.txt 计算特定样本群体的多态性; vcftools --vcf test.vcf --keep pop.list --window-pi <integer> --out out.txt ...
–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 ...
vcftools --vcf input_data.vcf --window-pi 10000 --window-pi-step 5000 --out pop1_vs_pop2 & 1. 2. 3. 4. 5. 转换成Plink格式: vcftools --vcf input_data.vcf --plink --chr 1 --out output_in_plink 1. (2)VCFtools在处理群体SNP数据时高效便捷 ...
--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. ...
--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. ...