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 >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.**science.biology.informatics.**conduc tor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >>> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]