On Sat, Sep 22, 2012 at 9:16 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 09/22/2012 04:54 AM, Michael Lawrence wrote:
>
>> 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).
>>
>
> unknown INFO and FORMAT fields now (v. 1.3.30) generate a warning and
> don't get parsed. Seems like FILTER and ALT don't currently get checked;
> are you looking for a warning on invalid value?
>
>
Sure, for the sake of consistency with the INFO/FORMAT fields.

Michael


> Martin
>
>
>
>> 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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