[Samtools-help] bcftools view, filter on AF

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

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



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.