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Re: [Vcftools-help] vcf-contrast issue
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From: Nijman, I.J. <I.N...@um...> - 2012-10-11 17:31:20
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Yes, such positions are there and also in the output file. But also real equal positions are in the output suggesting that something is not ok. Cheers ies Verstuurd vanaf mijn iPhone Op 11 okt. 2012 om 18:35 heeft "gowtham" <rag...@gm...<mailto:rag...@gm...>> het volgende geschreven: May be one of the sample does not have GT called at this base (due to lack of coverage). Did you look at the VCF file for these positions? Gowthaman On Wed, Oct 10, 2012 at 11:54 PM, Nijman, I.J. <I.N...@um...<mailto:I.N...@um...>> wrote: HI, I‘m trying to get tumor specific variants out of a (correctly validated) multi-sample vcf file by using vcf-contrast (vcf-contrast +tumor –ref multisample.vcf >tumor_spec.vcf). The issues is that there are a lot of error message while running, and the resulting tumor_spec.vcf is a complete copy of the original file. The errors are: Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25648. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25648. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25648. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25648. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25648. Argument "." isn't numeric in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25649. Argument "." isn't numeric in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25656. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25656. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25656. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25656. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25656. Use of uninitialized value in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25656. Argument "." isn't numeric in addition (+) at /usr/local/bin/vcf-contrast line 299, <$__ANONIO__> line 25657. I use release 785 svn revision of the vcftools, and vcf-contrast is r770. Am I missing something and how can I fix this issue? Cheers, Ies Nijman ******************************************************************************* I.J. Nijman, PhD Utrecht Medical Center | Department of Medical Genetics | Universiteitsweg 100 | 3584 CG | Utrecht | The Netherlands | phone +31 (0) 887568082<tel:%2B31%20%280%29%20887568082> / (+31) (0)6 29080780<tel:%28%2B31%29%20%280%296%2029080780> ******************************************************************************* ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ Vcftools-help mailing list Vcf...@li...<mailto:Vcf...@li...> https://lists.sourceforge.net/lists/listinfo/vcftools-help -- Gowthaman Bioinformatics Systems Programmer. SBRI, 307 West lake Ave N Suite 500 Seattle, WA. 98109-5219 Phone : LAB 206-256-7188 (direct). |
