Re: [Vcftools-help] depth filtering

[vijai2007 <20...@gm...>]

Adam,
Does the genotype filters work on the GT:AD:GQ:PL field? If only AD is
available per genotype and DP only as site specific averages, how do the
genotype filters work?
thanks
Vijai


On Tue, Dec 10, 2013 at 3:27 PM, Angela <ang...@gm...> wrote:

> Thanks, for the fast reply! all of them. I'm in the process of testing the
> different filters to see how they affect the data. This helps. I started
> off using only the genotype filter and filtered out nearly all of my SNPs.
> If I understand correctly then my min and max for the genotype filter
> should be set on a coverage I expect for each isolate, not the coverage
> that I would expect for all 24 combined. But for the site filter (top
> option) I would base it on what I expect for the group.
> Thanks very much
> Cheers
> Angela
>
> Sent from my iPhone
>
> On Dec 10, 2013, at 11:16 AM, Adam Auton <ada...@gm...> wrote:
>
> Not sure I follow. Which options are you referring to exactly?
>
> Site filters:
>
> --min-meanDP <float>
> --max-meanDP <float>
>
> Include sites with mean Depth within the thresholds defined by these
> options. These options calculate the mean depth at each site, averaged
> across individuals.
>
> Individual filters:
>
> --min-indv-meanDP <float>
> --max-indv-mean-DP <float>
>
> Calculate the mean coverage on a per-individual basis. Only individuals
> with coverage within the range specified by these options are included in
> subsequent analyses. These options calculate the mean depth in each
> individual across sites.
>
> Genotype filters:
>
> --minDP <float>
> --maxDP <float>
>
> Exclude all genotypes with a sequencing depth (DP) outside the range
> defined by these options. These options operate on each genotype
> individually.
>
>
> On 10 December 2013 14:10, Angie Dale <ang...@gm...> wrote:
>
>> Hello
>> I was wondering if there is somewhere I can find more information on the
>> depth filtering for vcftools. There are two options I am working with. The
>> genotype and site filters.
>>
>> Specifically I need to know the difference between these two filters and
>> how they are calculated - when I am using a multivcf file for 24
>> individuals are the mean calculations based on the mean of the 24 or still
>> per individual?
>> --
>> Angela Dale
>> PhD Candidate
>> TAIGA
>> Tree Agressors Identification using Genomics Approaches
>>
>> Forest Sciences Centre
>> University of British Columbia
>> 3621 - 2424 Main Mall, Vancouver, BC, V6T 1Z4 Canada
>> ang...@gm...
>> 778-689-3065
>>
>>
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>>
>
>
> --
> Adam Auton
> Assistant Professor,
> Department of Genetics,
> Albert Einstein College of Medicine,
> 1301 Morris Park Avenue,
> Van Etten B06,
> Bronx, New York 10461
>
> Tel: +1 (718) 839 7216
>
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
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