|
From: Barris, W. <Wes...@co...> - 2011-09-07 21:35:07
|
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
This email and any files transmitted with it are confidential and intended solely for the use of the addressee. If you are not the intended addressee, then you have received this email in error and any use, dissemination, forwarding, printing, or copying of this email is strictly prohibited. Please notify us immediately of your unintended receipt by reply and then delete this email and your reply. Cobb-Vantress, Inc. and its subsidiaries and affiliates will not be held liable to any person resulting from the unintended or unauthorized use of any information contained in this email or as a result of any additions or deletions of information originally contained in this email.
|