[Vcftools-help] site-mean-depth values do not correspond with min/max meanDP

[Óscar M. <om...@bi...>]

Dear all,

I'm using VCFtools 0.1.17 to filter out loci with low (or extremely 
high) coverage, and it is is surprisingly fast even with big data sets.

First I check the mean values (and plot them) to determine a range of 
mean depth, and then I filter out the loci out of that range.

example command line:

vcftools --vcf populations.snps.vcf --site-mean-depth --out 
dataset_m01r5p19R7h5

vcftools --vcf populations.snps.vcf --min-meanDP 4 --max-meanDP 20 
--recode --out dataset_m01r5p19R7h5_depth



Problem is the number of loci  with a specific depth are not the same in 
the ".ldepth.mean" table than in the output file after pruning loci.

For example: If I check how many loci there are with MEAN_DEPTH above 4; 
in the table there is 5926; but if I prune out loci with "--min-meanDP 
4" there are only 2157 loci left in the output file.

Tried this with many different data, and combinations of values for 
--min-meanDP and --max-meanDP, and I always get way fewer loci in the 
output file than if I calculate their number manually from the table.


What could be the reason of this? I can send you the log files or any 
other file if that helps.


Many thanks



-- 
Dr. Óscar Mira
Department of Biology
University of Zagreb
Rooseveltov trg 6
10000 Zagreb, Croatia