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cgroza / GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
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New variations after genotyping. #32

Closed tongyin121 closed 18 hours ago

tongyin121 commented 3 days ago

Hi,

Thank you for your excellent pipeline. I utilized a custom-made VCF file for genotyping. However, some variations were identified during the genotyping step. here are some examples: 屏幕截图 2024-07-01 164546.pdf The rows in the ID column that do not contain 'Chr' represent newly discovered mutations. Can these newly generated mutations be directly removed?

clemgoub commented 3 days ago

Hello @tongyin121,

Indeed, I believe these were added by GraphAligner? Is this from the GraffiTE.merged.genotypes.vcf file or a individual VCF? They can indeed be removed.

@cgroza, didn't we add a routine to remove these variants from the output?

Cheers,

Clément

cgroza commented 1 day ago

As of now there is no routine to remove them.

However, they have no TE annotation so they can easily be discarded.

Cristian Groza

On Monday, July 1st, 2024 at 12:44 PM, Clément Goubert @.***> wrote:

Hello @.***(https://github.com/tongyin121),

Indeed, I believe these were added by GraphAligner? Is this from the GraffiTE.merged.genotypes.vcf file or a individual VCF? They can indeed be removed.

@.***(https://github.com/cgroza), didn't we add a routine to remove these variants from the output?

Cheers,

Clément

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

tongyin121 commented 18 hours ago

Hello @tongyin121,

Indeed, I believe these were added by GraphAligner? Is this from the GraffiTE.merged.genotypes.vcf file or a individual VCF? They can indeed be removed.

@cgroza, didn't we add a routine to remove these variants from the output?

Cheers,

Clément

Yes, the data is from the GraffiTE.merged.genotypes.vcf file, and I will follow your advice to discard them.

tongyin121 commented 18 hours ago

As of now there is no routine to remove them. However, they have no TE annotation so they can easily be discarded. Cristian Groza … On Monday, July 1st, 2024 at 12:44 PM, Clément Goubert @.> wrote: Hello @.(https://github.com/tongyin121), Indeed, I believe these were added by GraphAligner? Is this from the GraffiTE.merged.genotypes.vcf file or a individual VCF? They can indeed be removed. @.(https://github.com/cgroza), didn't we add a routine to remove these variants from the output? Cheers, Clément — Reply to this email directly, [view it on GitHub](#32 (comment)), or unsubscribe. You are receiving this because you were mentioned.Message ID: @.>

Sure, I will discard them.