search

WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
224 stars 342 forks source link

Annnotated VCF missing new INFO headers #11

Closed sxv closed 8 years ago

sxv commented 8 years ago

When annotating with table_annovar.pl, my output VCF file contains several new entries in the INFO column, as expected. However these new INFO values are not added to the meta-information header lines at the top of the VCF file.

The VCF specification states "It is strongly encouraged that information lines describing the INFO, FILTER, and FORMAT entries used in the body of the VCF file be included in the meta-information section."

Several downstream VCF tools, including bcftools, require these INFO headers to be present in order to parse VCFs. So while they are technically optional, it seems like best practice to include them in the VCF output.

Thoughts?

kaichop commented 8 years ago

They should be included. If you can provide the command line and the example header that would be helpful.

On Tue, Apr 26, 2016 at 9:53 PM, sujay notifications@github.com wrote:

When annotating with table_annovar.pl, my output VCF file contains several new entries in the INFO column, as expected. However these new INFO values are not added to the meta-information header lines at the top of the VCF file.

The VCF specification states "It is strongly encouraged that information lines describing the INFO, FILTER, and FORMAT entries used in the body of the VCF file be included in the meta-information section."

Several downstream VCF tools, including bcftools, require these INFO headers to be present in order to parse VCFs. So while they are technically optional, it seems like best practice to include them in the VCF output.

Thoughts?

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/11

sxv commented 8 years ago

Is it possible this was fixed in a recent release? I am unable to reproduce this result with the new version of ANNOVAR, but my old annotated VCFs lack the INFO headers..

kaichop commented 8 years ago

Yes it is fixed in a previous release (not so recent though).

On Tue, Apr 26, 2016 at 10:18 PM, sujay notifications@github.com wrote:

Is it possible this was fixed in a recent release? I am unable to reproduce this result with the new version of ANNOVAR, but my old annotated VCFs lack the INFO headers..

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/11#issuecomment-214972149

sxv commented 8 years ago

Great, thanks for your lightning speed response!