Hello, I am a trying to filter some vcf files based off a set of rs#s (`$FILE` corresponds to chromosome #, so for now that is just 21, 22, and Y)

    vcftools --gzvcf "sorted_AltaiNea.hg19_1000g."$FILE".mod.vcf.gz" --snps 330k.txt --out "filtered_AltaiNea.hg19_1000g."$FILE"_"

I run that code on the cluster, but then all I get out are

    filtered_AltaiNea.hg19_1000g.21_.log
    filtered_AltaiNea.hg19_1000g.22_.log
    filtered_AltaiNea.hg19_1000g.Y_.log

Which contain text as such:

    VCFtools - v0.1.11
    (C) Adam Auton 2009
    
    Parameters as interpreted:
        --gzvcf sorted_AltaiNea.hg19_1000g.21.mod.vcf.gz
        --out filtered_AltaiNea.hg19_1000g.21_
        --snps 330k.txt
    
    Using zlib version: 1.2.3
    Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files.
    Index file is older than variant file. Will regenerate.
    Building new index file.
        Scanning Chromosome: 21
        Warning - file contains entries with the same position. These entries will be processed separately.
    
    Writing Index file.
    File contains 35104060 entries and 1 individuals.
    Applying Required Filters.
    Keeping sites by user-supplied list
    After filtering, kept 1 out of 1 Individuals
    After filtering, kept 5364 out of a possible 35104060 Sites
    Run Time = 176.00 seconds

I do not have any vcf output, just those log files. Is there something I am doing wrong? Thanks!
You should add the `--recode` flag to produce a new vcf file.

See example 2 on http://vcftools.sourceforge.net/man_latest.html