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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Computation of INFO tags in bcftools +fill-tags #2107

Closed nirav572 closed 4 months ago

nirav572 commented 5 months ago

When utilizing bcftools +fill-tags, is the computation of various INFO tags performed every time the command is executed, or only when INFO columns are empty?

For instance, if I reduce the dataset to fewer samples and wish to recalculate AC/AF/AN, what would be the best way to go about it?

Some clarification regarding this would be helpful on the documentation page as well. Thank you!

pd3 commented 4 months ago

If you are removing samples using bcftools view --samples , then INFO/AC and INFO/AN are updated automatically. The rest (INFO/AF) will be updated only with bcftools +fill-tags and there is no speed penalty if it simultaneously updates also AC,AN again.

nirav572 commented 4 months ago

Thank you!