Question: SNPEff missing annotations from VCF?
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gravatar for vctrm67
12 months ago by
vctrm6710
vctrm6710 wrote:

I have an annotated VCF file (in SNPEff format). I noticed that the SNPEff format does not provide information regarding the SVType in the INFO section, whereas the VCF format does. Is there a way to recover this information?

For background, I am trying to convert vcf.snpeff file to a bedpe file using the SVTools vcftobedpe module, but it seems that I will have to modify the vcf.snpeff to vcf manually first.

snpeff vcf • 259 views
ADD COMMENTlink written 12 months ago by vctrm6710

Hello,

can you show us what you mean by "SNPEff format"? Usually the output of SnpEff is a valid vcf file.

fin swimmer

ADD REPLYlink written 12 months ago by finswimmer13k

It is simply an SnpEff annotated VCF file that ends with .vcf.snpeff.

Alternatively, are there any tools that convert SnpEff files to BedPE files?

ADD REPLYlink written 12 months ago by vctrm6710

Please show the commands used for generating you snpeff vcf file.

snpeff just adds information to your vcf and should not remove some.

Also some example lines of your "normal" vcf file and the snpeff vcf file would be useful.

ADD REPLYlink written 12 months ago by finswimmer13k
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