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Remove overlaps not working as expected

Open mbhall88 opened this issue 1 year ago • 6 comments

I'm not sure if I am misunderstanding how bcftools +remove-overlaps works, but I still have some overlapping variants in the output afterwards

e.g.,

chromosome      28728   62e866df        T       A       .       PASS    .      GT      1/1
chromosome      28728   e4388ae3        T       TA      .       PASS    .    GT      1/1

and

chromosome      30586   60f6a01c        T       TAACAACACTTGG   .       PASS    .      GT      1/1
chromosome      30588   a1f621d4        G       A       .       PASS    .    GT      1/1

mbhall88 avatar Jan 24 '24 00:01 mbhall88