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                                            Livia Moura

Subsetting for A-length annotations (e.g. AF, PRI, F1R2, F2R1),

Hello @ldgauthier. Just to let you to know what we tested so far, and what was working.... 1 - Reblock with the snapshot + pipe with gnarly SNAP --> working...

Subsetting for A-length annotations (e.g. AF, PRI, F1R2, F2R1),

Haha.. It's not about faith.. For now, I really don't know why I should use gnarly as a step, instead of GenotypeGVCF right away (with usegnarly = false). As gnarly...

Subsetting for A-length annotations (e.g. AF, PRI, F1R2, F2R1),

Excelent... good job I'm glad that I read "is more sensitive to rare alleles at common sites". As we are working with rare diseases, this is gold. Ok... I'm convinced...