bcftools
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Remove overlaps not working as expected
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