根据ALLEL进行过滤 –maf,–max-maf Minor Allele Frequency二等位基因频率进行过滤,常为–maf 0.05,保留大于0.05的。 –non-ref-af,–non-ref-ac… 保留都是ALT变异的位点。 –mac INT,–max-mac 保留Minor Allel Count数大于INT数的位点 –min-alleles 2, --max-alleles 2筛选保留含有2个ALT变异的位点。...
ALLELE FILTERING --maf 和 --max-maf用来限定最小等位基因频率(MAF)的范围 --mac 和 --max-mac和上面类似,用来限定最小等位基因的数量 --min-alleles 和 --max-alleles用来限定等位基因的数量,比如这条命令只会保留vcf文件ALT列只有一种碱基的情况。 vcftools --gzvcf combined200.vcf.gz --min-alleles 2...
Includes or excludes all sites with a specific INFO flag. These options only filter on the presence of the flag and not its value. These options can be used multiple times to specify multiple INFO flags.自己理解下就好 根据ALLELE过滤 –maf MAF最小值过滤 –max-maf MAF最大值过滤 此处省去很多...
2. 计算Allele Frequency: vcftools --vcf input_data.vcf --freq --out output 1. 提取测序深度 vcftools --vcf input_data.vcf --depth -c > depth_summary.txt vcftools --vcf input_data.vcf --site-depth --max-missing 1.0 --out site_depth_summary ## SNP中不允许样本基因型缺失 1. 2. 计...
根据ALLELE过滤 –maf <float> MAF最小值过滤 –max-maf <float> MAF最大值过滤 此处省去很多参数,具体参见vcftools官网 根据基因型数值过滤 –min-meanDP<float> –max-meanDP <float>根据测序深度进行过滤 –hwe<float> –max-missing <float>完整度,该参数介于0,1之间 ...
2 --max-alleles 2 \ --remove-indels 2>vcftools.log| gzip - >myresult/nohup1.vcf.gz & ...
ALLELE FILTERING --maf--max-maf Include only sites with a Minor Allele Frequency greater than or equal to the "--maf" value and less than or equal to the "--max-maf" value. One of these options may be used without the other. Allele frequency is defined as the number of times an ...
--non-ref-af <float> --max-non-ref-af <float> Include only sites with Non-Reference Allele Frequency within the specified range. --hue <float> Assesses sites for Hardy-Weinberg Equilibrium using an exact test, as defined by Wigginton, Cutler and Abecasis (2005). Sites with a p-value ...
Include only sites with all Non-Reference (ALT) Allele Frequencies greater than or equal to the "--non-ref-af" value and less than or equal to the "--max-non-ref-af" value. One of these options may be used without the other. Allele frequency is defined as the number of times an ...
Allele count is simply the number of times that allele appears over all individuals at that site. --min-alleles <integer> --max-alleles <integer> Include only sites with a number of alleles greater than or equal to the "--min- alleles" value and less than or equal to the "--max-...