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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