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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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If I put two adjacent small variants together, will it be divided into two variants by "bcftools norm"? #2027

Closed tanger-code closed 10 months ago

tanger-code commented 10 months ago

Hi. If I put two adjacent small variants together, will it be represented separately when it's normalized? For example, if I have 2 SNPs:

chrom     pos     ref    alt
chr1      100     A      G
chr1      102     C      T

And I represent them jointly like this：

chrom   pos     ref     alt
chr1    100     ANC     GNT

When I use bcftools norm command, will it be divided into two variants?

pd3 commented 10 months ago

If and only if you run with the -a, --atomize option, then yes :)