Re: [Samtools-help] bcftools view, filter on AF

[Tommy C. <tc...@sa...>]

Hi Petr,

Thank you very much for your speedy reply. I opted to use multiple pipes
to be on the safe side.

Thanks,
Tommy

On 04/10/2016 15:07:45, "Petr Danecek" <pd...@sa...> wrote:

>Hi,
>
>if I remember correctly the -i/-e options are applied before and
>--max-af after subsetting. If unsure, or if a different behaviour is
>needed, it is possible to stream multiple commands to make it explicit:
>
>$bt view -e .. -Ou | $bt view -s ..
>
>petr
>
>
>On Tue, 2016-10-04 at 13:56 +0000, Tommy Carstensen wrote:
>> To samtools-help,
>> 
>> 
>> Is this list also for questions related to bcftools?
>> 
>> 
>> The documentation for the tool PLINK lists the sequence in which
>> command line flags are executed:
>> https://www.cog-genomics.org/plink2/order
>> 
>> 
>> Is there a similar page for bcftools?
>> 
>> 
>> The reason I'm asking, is because I'm filtering out samples and then
>> filtering based on AF.
>> 
>> 
>> 1) Can I use either of the two methods below?
>> 2) Will the AF be calculated for the filtered samples only? Or is the
>> AF evaluated prior to sample filtering?
>> 
>> 
>> bcftools view --exclude AF<0.1
>> bcftools view --max-af 0.1
>> 
>> 
>> Thank you very much.
>> 
>> 
>> Tommy
>
>




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