Question: MAF option in vcftools
gravatar for thjnant
4.9 years ago by
thjnant90 wrote:


I am trying to run this command on my vcf files:

vcftools --gzvcf LcovEx_africa.vcf.gz --maf 0.05 --out filtered.out

It seems to be working fine, however, it does not print out the output file but only the log file, please see below. 

As I have been using these vcf files for several other purposes and utilities of the vcftools such as calculating Fst and it has been working fine, I am wondering what the problem could be here. 

Thank you very much in advance for your help,



VCFtools - v0.1.11

(C) Adam Auton 2009

Parameters as interpreted:

--gzvcf LcovEx_africa.vcf.gz

--maf 0.05

--out filtered.out

Using zlib version:

Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files.

Reading Index file.

Building new index file.

Scanning Chromosome: 1

Writing Index file.

File contains 2550621 entries and 150 individuals.

Applying Required Filters.

Filtering sites by allele frequency and call rate

After filtering, kept 150 out of 150 Individuals

After filtering, kept 649848 out of a possible 2550621 Sites

Run Time = 1486.00 seconds
vcftools • 5.3k views
ADD COMMENTlink modified 4.8 years ago by Giovanni M Dall'Olio26k • written 4.9 years ago by thjnant90

I just want to clarify the problem you're experiencing. Your title mentions the Minor Allele Frequency parameter, but it seems your core problem is that the vcftools program is not creating output.

You said: however, it does not print out the output file but only the log file

The behavior I would expect to see from your command is that a file named filtered.out would be created (not printed to stdout), and that the program feedback would be printed to stdout.

When you run ls in the same directory that you were in when you ran the vcftools command, you do not see filtered.out, is that correct? When you run vcftools with different parameters, is it writing the output file?

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Dan D6.7k
gravatar for Giovanni M Dall'Olio
4.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

Just add the --recode option:

vcftools --gzvcf LcovEx_africa.vcf.gz --recode --maf 0.05 --out filtered.out
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Giovanni M Dall'Olio26k
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