Dear Hugo,
Thanks so much! It worked when I made the #contig= lines from both target and ref vcfs common (included the lines of both in same order) as you suggested. Wonderful. I checked the github bug and fix link, may I just clarify from you I didn't get how come it's fixed 2 weeks ago but isnt working still? does this mean when a newer release/version is available it won't have this bug or is it that when a bug is fixed there's something manual we need to change in the current tool directories/code ? (I downloaded impute5 less than 2 weeks ago, so that's after the fix, that's why i'm confused, however your suggestion worked nicely, but i just wanted to understand what generally should be done when a bug is fixed on github but apparently still not working)
Many thanks for all your time and support. You've helped me greatly.
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