Question: SNPEff missing annotations from VCF?
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gravatar for vctrm67
10 weeks ago by
vctrm670
vctrm670 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 • 124 views
ADD COMMENTlink written 10 weeks ago by vctrm670

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 10 weeks ago by finswimmer12k

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 10 weeks ago by vctrm670

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 10 weeks ago by finswimmer12k
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