Comments (3)
tseemann
commented on June 9, 2024
@sbaines is this value you want just the size of core.aln divided by size of core.full.aln ?
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sbaines
commented on June 9, 2024
Hi Torsten,
The current stats I use most often are %core (for all sites) and %core-variants, both of which I can source from snippy + afa-core.pl. If the calculations from the later (no need to write the core files) could be incorporated in snippy it would be useful (one-stop-shop), but not essential.
Sarah
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tseemann
commented on June 9, 2024
@sbaines
FYI I don't use afa-core.pl anymore in nullarbor. I have migrated to snp-sites -c. This runs 1000x faster which makes a big difference for huge alignments.
Ok, I think I understand what you need now. I will try and implement!
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