vcf_consensus_error:Conflicting_variants

[cucurbit]

Hi there,

I'm trying to add indels from a vcf file, to the reference fasta file, in order to create a new reference. For that, I use bgzip, tabix and finally vcf-consensus tool. But I'm getting the following error:

"Note: Conflicting variants at (or near) 'positionXXX', cannot apply both."

Any ideas of the meaning of these error?

Thanks

Iran

[cariboudoug]

Hey,

Is it possible there is an insertion in one individual in a region deleted in another individual?

[rajeshkmaurya08]

Hi,
I am also getting some problem while using vcf-consensus...
i used command
cat chr21.fa | vcf-consensus chr21_a.vcf.gz > chr21_ref21.fa

but i got following error.

The sequence "21" not found in the fasta file.

can anyone help me to resolve this issue.