–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。常用。 根据基因型G...
vcftools --gzvcf combined200.vcf.gz --diff output_noMissing.recode.vcf --diff-site --out in1_v_in2 下面的表头的1、2分别表示文件1、文件2,第4列1或2表示仅文件1或文件2有,B表示都有 $ head in1_v_in2.diff.sites_in_filesCHROMPOS1POS2IN_FILEREF1REF2ALT1ALT2chr111467101146710BGGAAchr1...
and private doubletons (i.e. SNPs where the minor allele only occurs in a single individual and that individual is homozygotic for that allele). The output file has the suffix “.singletons”.
The output file will be written tooutput.frq. Getting sequencing depth information Another useful output functionsummarizes sequencing depthfor each individual or for each site. Just like the allele frequency example above, this output function follows the same basic model. ./vcftools --vcf input_da...
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 think...
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 & ...
./vcftools --vcf input_data.vcf --freq --out output The output file will be written tooutput.frq. Getting sequencing depth information Another useful output functionsummarizes sequencing depthfor each individual or for each site. Just like the allele frequency example above, this output function ...
plink, vcftool计算等位基因频率(allele frequency,vcf)