Does `table_annovar.pl -vcfinput` intentionally change character encoding? about doc-annovar

[kaichop]

Yes it is intentional, to differentiate the regular = notation in VCF specification and the "=" within a specific field.

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On Fri, Sep 7, 2018 at 4:56 PM, tkoomar ***@***.***> wrote: I do not know if this is a feature, bug, or user error. When providing a VCF to ANNOVAR via table_annovar.pl -vcfinput the output VCF has altered character encoding for punctuation that is part of some annotations -- i.e. ";" becomes "\x3b" and "=" becomes "\x3d" (illustrated by excerpted portions of multianno.txt and .vcf files below) From the VCF specification, these characters are reserved as delimiters and should not appear within individual INFO fields. So, while I can see that this behavior may be intentional, I was unable to determine from documentation if this is indeed the case. *multianno.txt* Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene 1 10469 10469 C 0 intergenic NONE;DDX11L1 dist=NONE;dist=1405 1 10469 10469 C G intergenic NONE;DDX11L1 dist=NONE;dist=1405 *multianno.vcf* #CHROM POS ID REF ALT QUAL FILTER INFO 1 10469 rs370233998 C * 2026.12 GATKCutoffSNP ANNOVAR_DATE=2018-04-16;Func.refGene=intergenic;Gene.refGene=NONE\x3bDDX11L1;GeneDetail.refGene=dist\x3dNONE\x3bdist\x3d1405 1 10469 rs370233998 C G 2026.12 GATKCutoffSNP ANNOVAR_DATE=2018-04-16;Func.refGene=intergenic;Gene.refGene=NONE\x3bDDX11L1;GeneDetail.refGene=dist\x3dNONE\x3bdist\x3d1405 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#41>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuLVcoIxAibZDRzL4cgARxaX1GexLks5uYt2RgaJpZM4Wfd2M> .

[tkoomar]

Excellent, thank you for the clarification.

A statement of this (perhaps in docs/articles/VCF.md) might be a nice heads up to new users like myself, but any issue one might have with this behavior can be solved easily enough using sed before bgzipping the resulting VCF. Closing this issue.