lower SNP overlap rate between call set and GATK results.

[ttian627]

Hello,

I find there are a fewer SNP overlap rate between the callset form pangenome-graph-from-assemblies and the GATK results. What could be the reason? The article seems to only compare the ability of genotyping and wether pangenie can identify most of the variants between assemblies.

Best,

Tian

[eblerjana]

PanGenie itself is a genotyper and not a variant caller and cannot detect any variants. It genotypes variants previously detected across other samples (for which haplotype-resolved assemblies are available). The "pangenome-graph-from-assemblies" pipeline is one way to generate such input VCFs for PanGenie.

GATK is a variant caller and thus can detect variants from short reads.

Can you please provide more details on what exactly you are comparing and how that data was generated?

[ttian627]

Hello，

I run the "pangenome-graph-from-assemblies" pipeline to identify variants and use PanGenie to genotype these variants on a panel of maize population. At the samle time, I used GATK to call variants on the same population. After filtered with samle parameters，I find these two variant sets with a few overlaped SNP locus. Maybe, I need other variant caller to identify more variants.

Best,

Tian

At 2024-05-24 19:53:44, "Jana Ebler" @.***> wrote:

PanGenie itself is a genotyper and not a variant caller and cannot detect any variants. It genotypes variants previously detected across other samples (for which haplotype-resolved assemblies are available). The "pangenome-graph-from-assemblies" pipeline is one way to generate such input VCFs for PanGenie.

GATK is a variant caller and thus can detect variants from short reads.

Can you please provide more details on what exactly you are comparing and how that data was generated?

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