VCF file comparison

[shmibble]

Hi,
I am trying to compare two VCF files (one created using bcftools and one created using freebayes. If you have an opinion on which is better that would be nice too) using vcf-compare. I sorted them (though i'm not sure if this was necessary) and compressed using bgzip. When I use vcf-compare i get the following error:

The version "4.2" not supported, assuming VCFv4.1
Warning: Read 0 lines from a.vcf.gz, the tabix index may be broken.
Warning: Read 0 lines from b.vcf.gz, the tabix index may be broken.

Any idea on how to solve this? I tried finding a way to get v4.1 VCF files but couldn't.

Thanks for the help!

[GenoMax]

Have you indexed them with tabix (as the error is indicating above)?

[Len Trigg]

You should absolutely be using rtg vcfeval to perform the comparison, as it correctly handles the differences in variant representation that different callers produce. Other comparison tools do not handle these differences. vcfeval is part of RTG Tools (free for anyone) and RTG Core (free for non-commercial use, and includes sophisticated variant calling you may also want to use).

[shmibble]

Geno, I did index them with Tabix although now that I think of it I didn't direct the output anywhere... Silly me. I'm guessing that should fix it although I cant check right now...
Len, thanks for the tip. I'll definitely try it out.

Thanks!

[shmibble]

Hi again. So I did index them correctly (I think). A new tbi file (a.vcf.gz.tbi) was created for each VCF. Still not sure why it's not working...