I have a variant record that looks like
Following bcftools norm --atomize ... (v1.16), it remains the same. I suppose this is an odd case, as the expected output for making them independent records would be the somewhat unintuitive
1 3552597 . C G
1 3552597 . C CGGG
I think it's a sensible expectation. I am trying to make a SNP matrix for a phylogenetic tree and this sample is not getting grouped with others that just have the C->G SNP when I do bcftools merge.