How vcftools removes or retains samples in vcf files

Editor to share with you vcftools how to remove or retain samples in the vcf file, I believe most people do not know much about it, so share this article for your reference, I hope you can learn a lot after reading this article, let's go to know it!

Vcftools removes or retains samples from vcf files

Vcftools can remove or retain samples from the vcf file with the options-- indv and-- remove-indv, specifying which samples to retain or delete from the vcf file. You can use this option multiple times to specify multiple samples.

The specific usage is as follows:

Keep only two samples 1 and 10, and execute the following code:

Vcftools-vcf in.vcf-recode--recode-INFO-all-stdout-indv 1-indv 10 > out.vcf

Delete sample 1 and execute the following code:

Vcftools-vcf in.vcf-recode--recode-INFO-all-stdout-remove-indv 1 > out.vcf

If there are a large number of samples, you can also save the samples to the file id.txt, with one sample ID for each behavior, in the following format:

1105

Then use the following two options to retain or delete samples from the vcf file.

-- keep retention sample

-- remove deletes samples

The code is as follows:

Vcftools-- vcf in.vcf-- recode--recode-INFO-all-- stdout-- keep id.txt > out.vcf are all the contents of this article entitled "how to remove or retain samples from vcf files by vcftools". Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!