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We have received reports of a bug occurring with HaplotypeCaller in v2.4, with the error message "Reads are too small for use in assembly." We are working to fix it.
In the meantime, if you encounter it too, please don't post a new discussion about it, but do post a comment on this announcement so that we can count how many people are affected.
Thank you for your patience and our apologies for the inconvenience!
Geraldine Van der Auwera, PhD