[Vcftools-help] what is min-meanDP?

[Barris, W. <Wes...@co...>]

I would like to filter a .vcf file so that the output contains variations
with a minimum read depth.  I have tried the --min-meanDP flag like this:

vcftools --vcf affected.vcf --chr chr10 --minQ 40 --min-meanDP 10 --out test --recode --keep-INFO-all

VCFtools - v0.1.6
(C) Adam Auton 2009

Parameters as interpreted:
        --chr chr10
        --keep-INFO-all
        --min-meanDP 10
        --minQ 40
        --out test
        --recode
        --vcf affected.vcf

Scanning affected.vcf ...
Currently scanning CHROM: chr10
        Completed reading required chromosome. Skipping remainder of file.
        Keeping 121484 entries (out of 121485 read)
Done
Filtering sites with Quality less than 40
Filtering sites by mean depth
Kept 1 out of 1 Individuals
Kept 0 out of 121484 Sites
Error:No data left for analysis!

As you can see, nothing was output.  The vcftools documentation does not
go into much detail about this flag.  Isn't this the correct flag to use
to filter on read depth?
-- 
Wes Barris


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