Just in case you don't know, it is possible to work around this using the
"info" slot of ScanVcfParam. But yes having a simple option to ignore
unknown INFO and FORMAT fields would be convenient. The same should also
apply to FILTER and ALT (in the case of structural variants).

Michael

On Fri, Sep 21, 2012 at 10:51 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> Hi, Val.
>
> Is there in interest in simply ignoring unknown INFO and GENOTYPE fields
> when parsing VCF files, perhaps by issuing a warning instead of an error?
>  There are LOTS of malformed VCF files out there.  In some cases, they are
> not useable, but in this case, they can be perfectly useable if these
> unknown fields are simply ignored.
>
> > dat = readVcf('tmp.gatk.vcf',genome='hg19')
> Error: scanVcf: record 22 INFO 'KGPilot123' not found
>   path:
> /Volumes/CCRBioinfo/projects/RosenbergImmuneStudy/staging/tmp.gatk.vcf
>
> Thanks,
> Sean
>
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