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some issue about nan #4

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shenhaizhongdechanrao opened this issue Mar 13, 2024 · 1 comment
Open

some issue about nan #4

shenhaizhongdechanrao opened this issue Mar 13, 2024 · 1 comment

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@shenhaizhongdechanrao
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Hello, I am trying to construct a tree using the VCF file obtained from merging with GATK and bcftools. After using the VCF2Dis command to generate a .mat file, but there are many '-nan' in the result. Can you give me some suggestions?
@hewm2008
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You have too few vcf sites and too many miss genotypes.
It is recommended to generate vcf directly from gvcf merging instead of bcftools merging, because this will cause many sites to be missed.

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@hewm2008 @shenhaizhongdechanrao