Re: [Vcftools-help] vcf-contrast issue

[gowtham <rag...@gm...>]

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...>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 / (+31)
> (0)6 29080780
>
> *******************************************************************************
> ****
>
> ** **
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-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).