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From: Mario D. <mar...@go...> - 2011-11-23 12:16:18
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Hello everyone, at the moment I am trying to use the vcf-annotate command. I call it like this zcat Normal5.vcf.gz | vcf-annotate -f d=4/D | bgzip -c > Normal5_filtere.vcf.gz But then I get an error like this: Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 27. Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 28. Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 29. Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 30. Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 31. Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 32. Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 33 ... It doesn't matter which files I input. The input is generated by GATK. Also I don't get errors or warnings while compiling VCF-Tools. Every other command works fine, also the PERL Path is exported. When I run the validator, I don't get error. Any ideas? With best, Mario __ md mar...@go... |