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".
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
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:
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.
Thank you I will try it!
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
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:
According to the vcftools manual:
Hope it helps!
Thank you for your post! I was having the same trouble and the --recode option worked!