SNPEff missing annotations from VCF?

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5.3 years ago

vctrm67 ▴ 80

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 • 1.1k views

ADD COMMENT • link 5.3 years ago by vctrm67 ▴ 80

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Hello,

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

fin swimmer

ADD REPLY • link 5.3 years ago by finswimmer 16k

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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 REPLY • link 5.3 years ago by vctrm67 ▴ 80

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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 REPLY • link 5.3 years ago by finswimmer 16k

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