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bcftools norm --atomize does not split up a SNP followed by an insertion #1832

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0xaf1f opened this issue Dec 7, 2022 · 1 comment
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@0xaf1f
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0xaf1f commented Dec 7, 2022

I have a variant record that looks like

1       3552597   .       C       GGGG

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.

@pd3 pd3 closed this as completed in 1f50f07 Jan 3, 2023
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pd3 commented Jan 3, 2023

That's a fair point, addressed now by 1f50f07. Thanks for the issue

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