Filtering a vcf file with vcftools, where is my output?

Question

[devenvyas]

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!

Answer 1

[chefer]

You should add the --recode flag to produce a new vcf file.

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

[firestar]

You must be kidding me!

[Shicheng Guo]

so what happened if we don't add --recode? if just delete the SNPs from the raw input?