SnpEff question for Variant annotation
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20 months ago

I have a annotated my VCF using SnpEff and now I want to convert INFO column into different columns. Can anybody suggest any tool or command?

gene next-gen vcf snpeff • 354 views
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an example of output is needed

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Here is the example :

DP=219;MQ=25.33;TLOD=44.88;FractionInformativeReads=0.530;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*268G>A|||||268|,A|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2692C>T|||||2692|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*1007G>A|||||1007|,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1254-176C>T||||||
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that's the input. we need the output

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That looks like an INFO column with SnpEff annotation to me.

mandar.bedse Which output format (columns/structure) do you want to get from that? You'll have to be more specific.

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Do you mean you want to have the output from SNPEff to be converted into a tab separated file?

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Yes, I want to convert the output from SNPEff to be converted into a tab-separated file?

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How should that tab-separated file look like? You'll have to be more specific!

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