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@brentp brentp released this 26 Mar 16:56
· 30 commits to master since this release

this release adds support for CSI. this can greatly speed up dense files like CADD and even gnomAD or ExAC.

to use, simply index your file with tabix as, e.g.:

tabix -m 12 --csi $file

and vcfanno will prefer the .csi index over the .tbi.

refer to the performance page for how to optimize.
in brief, setting

export IRELATE_MAX_GAP=1000

seems to give good results. Please experiment and let me know what works for you. I can get ~60% speed improvement using csi'd ExAC to annotate clinvar with the above changes.