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This article mainly introduces "vcftools filtering how to specify the variation site of the deletion rate". In the daily operation, I believe that many people have doubts about how to specify the variation site of the deletion rate by vcftools filtering. The editor consulted all kinds of data and sorted out a simple and easy-to-use operation method. I hope it will be helpful for you to answer the doubt of "how to specify the mutation site of the deletion rate by vcftools filtering"! Next, please follow the editor to study!

A lot of snp in vcf file is missing in some samples, that is, the genotype is ". /." If the deletion rate is high, this snp locus cannot be used in many analyses and needs to be removed. At this point, you can use vcftools for filtering. The option used is-- max-missing.

The specific usage is as follows:

Run the following command:

Vcftools-vcf snp.vcf-recode--recode-INFO-all-stdout-max-missing 1 > snp.new.vcf

-- max-missing is followed by a value of 0-1, 1 means not allowed to be missing, 0 means all are allowed to be missing

Finally, there is no deletion of snp loci in the vcf file.

At this point, the study on "how to specify the mutation site of deletion rate by vcftools filtering" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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