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。...
2.3 vcf文件过滤 vcftools --vcf root.hic.id.vcf --max-missing 0.8 --maf 0.05 --min-alleles 2 --max-alleles 2 --recode --recode-INFO-all --out root.hic.id.int0.8maf0.05.allele2 max-missing:分型完整度 maf:第二等位基因频率 min-alleles:最小等位基因个数 max-alleles:最大等位基因个数 ...
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...
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 根据材料过滤 –indv –remove-indv...
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 ...
--min-meanDP <float> --max-meanDP <float> Include sites with mean Depth within the thresholds defined by these options. --maf <float> --max-maf <float> Include only sites with Minor Allele Frequency within the specified range. --non-ref-af <float> --max-non-ref-af <float> Include...
--max-non-ref-ac Include only sites with all Non-Reference (ALT) Allele Counts greater than or equal to the "--non-ref-ac" value and less than or equal to the "--max-non-ref-ac" value. One of these options may be used without the other. Allele count is simply the number of ...
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-...