How to delete sample using vcftools

Question

[chengyi31000]

If I had merged every vcf file of samples, but find one sample I don't want. How can I delete that sample using vcftools?? Thank you!!!

Answer 1

[Philipp Bayer]

As it says in the manual

--indv <string>
--remove-indv <string>

Specify an individual to be kept or removed from the analysis. This option can be used multiple times to specify multiple individuals. If both options are specified, then the "--indv" option is executed before the "--remove-indv option".

So for example (untested)

vcftools --remove-indv YOUR_INDIVIDUALS_NAME --vcf your_snps.vcf --out your_filtered_snps.vcf

[chengyi31000]

Thank you I will try it!

[chengyi31000]

It seems work But I can't find the output file?? There only a .log file.

Parameters as interpreted: --vcf /home/chung/vcftools_0.1.13/perl/QC/life_chr2.vcf --out /home/chung/vcftools_0.1.13/perl/QC/life_chr2_new.vcf --remove-indv NGS20140306D

Excluding individuals in 'exclude' list After filtering, kept 420 out of 421 Individuals After filtering, kept 2609042 out of a possible 2609042 Sites Run Time = 93.00 seconds

[catalina.ramirez.portilla]

Hi! I was having the same trouble but if your just add --recode to your line, it will generate the file with the prefix you stated with --out. Like this:

vcftools --remove-indv YOUR_INDIVIDUALS_NAME --vcf your_snps.vcf --recode --out your_filtered_snps.vcf

According to the vcftools manual:

These options are used to generate a new file in either VCF or BCF from the input VCF or BCF file after applying the filtering options specified by the user.

Hope it helps!

[Maggie Jia]

Thank you for your post! I was having the same trouble and the --recode option worked!