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?