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Vcf-Compare Vcftools Error

Hello,

I'm using VCFtools to compare 2 different vcf files. When I run vcf-compare with the following command:

vcf-compare Software/snpEff/chr11snps.vcf.gz Software/snpEff/chr11snps_output.vcf.gz

I get the following error:

Can't exec "tabix": No such file or directory at Software/VCFtools/perl/Vcf.pm line 2515. The command "tabix -l Software/snpEff/chr11snps.vcf.gz" exited with an error. Is the file tabix indexed? at Software/VCFtools/perl/Vcf.pm line 171 Vcf::throw('Vcf4_1=HASH(0x10092bdb0)', 'The command "tabix -l Software/snpEff/chr11snps.vcf.gz" exite...') called at Software/VCFtools/perl/Vcf.pm line 2516 VcfReader::get_chromosomes('Vcf4_1=HASH(0x10092bdb0)') called at Software/VCFtools/vcf-compare line 181 main::compare_vcfs('HASH(0x10082adb8)') called at Software/VCFtools/vcf-compare line 19

The files I'm using were previously compressed and indexed with gbzip and tabix, respectively. Does anyone know why it gives this error or whether there is a better way to compare vcf files?

vcftools
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written by Leandro Batista • Leandro Batista

Did you use "tabix -p vcf <file.vcf.gz>"?

• 0 views • link
written by Mdeng Mdeng

Just a guess: did export the perl variable? "export PERL5LIB=/path/to/your/installation/perl"

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written by Mdeng Mdeng

you can start by validating both the VCF files. vcf-validator example.vcf Can you run the other commands such as vcf-stats etc on these files?

• 0 views • link
written by jvijai jvijai

It works just fine with both vcf-validator and vcf-stats. I really cannot understand what is the problem.

• 0 views • link
written by Leandro Batista • Leandro Batista

do you have the tabix program in your PATH?

• 0 views • link
written by Sophia • Sophia

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