Question: Vcf-Compare Vcftools Error
0
gravatar for Leandro Batista
7.0 years ago by
Paris
Leandro Batista100 wrote:

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 • 4.0k views
ADD COMMENTlink written 7.0 years ago by Leandro Batista100
1

do you have the tabix program in your PATH?

ADD REPLYlink written 7.0 years ago by Sophia300

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

ADD REPLYlink written 7.0 years ago by Mdeng520

Yes, that's exactly what I used.

ADD REPLYlink written 7.0 years ago by Leandro Batista100

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

ADD REPLYlink written 7.0 years ago by Mdeng520

Yep, I've also done that!

ADD REPLYlink written 7.0 years ago by Leandro Batista100

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?

ADD REPLYlink written 7.0 years ago by jvijai1.1k

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

ADD REPLYlink written 7.0 years ago by Leandro Batista100
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