This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to delete sample using vcftools

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!!!

vcftools delete sample vcf
• 20,185 views • link
updated by Philipp Bayer Philipp Bayer • written by chengyi31000 • chengyi31000

1 answer

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
• 0 views • link
written by Philipp Bayer Philipp Bayer

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

• 0 views • link
written by chengyi31000 • chengyi31000

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!

• 0 views • link
written by catalina.ramirez.portilla • catalina.ramirez.portilla

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

• 1 views • link
written by Maggie Jia • Maggie Jia

Log in to answer this question.

More posts like this