MAF option in vcftools

Question

[thjnant]

Hello,

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,

Best,
Homa

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: 1.2.3.4
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

[Dan D]

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?

Answer 1

[Giovanni M Dall'Olio]

Just add the --recode option:

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