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!
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!
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