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。...
vcftools --vcf test1.vcf --diff test2.vcf --out compare Getting allele frequency 使用--freq计算等位基因频率 1 vcftools --vcf test.vcf --freq --out output 1 2 3 4 CHROM POS N_ALLELES N_CHR {ALLELE:FREQ} chr1 861315 2 604 G:0.996689 A:0.00331126 chr1 865655 2 604 T:0.998344 A:...
-1 I have a VCF file containing individuals belonging to different populations and I am trying to get allele frequencies for each population. Is there a way of obtaining this? My understanding is that --freq will give allele frequencies based on all the individuals. The only option I could...
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. 计算LD:...
一、安装 conda install -c bioconda vcftools 二、功能概览 常用功能如下,待具体用到时再做详细补充: Get basic file statistics Applying a filter Writing to a new VCF file Converting a VCF file to BCF Getting allele frequency Getting sequencing depth information ...
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。
Getting allele frequency To determine the frequency of each allele over all individuals in a VCF file, the--freqargument is used. ./vcftools --vcf input_data.vcf --freq --out output The output file will be written tooutput.frq.
Output allele frequency for all sites in the input vcf file from chromosome 1 vcftools --gzvcf input_file.vcf.gz --freq --chr 1 --out chr1_analysis Output a new vcf file from the input vcf file that removes any indel sites vcftools --vcf input_file.vcf --remove-indels --recode -...
Addition of "any" options to filter by frequency or count of any alternate allele (instead of requiring all of them to pass) Improvements to temporary file handling for all LD functions Added --chrom-map option to allow user specified chromosomes for writing out plink files ...
2 --max-alleles 2 \ --remove-indels 2>vcftools.log| gzip - >myresult/nohup1.vcf.gz & ...