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Old 05-28-2014, 08:00 AM   #1
cucurbit
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Location: Barcelona

Join Date: May 2014
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Default vcf_consensus_error:Conflicting_variants

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
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Old 05-28-2014, 08:14 AM   #2
cariboudoug
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Hey,

Is it possible there is an insertion in one individual in a region deleted in another individual?
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Old 02-21-2017, 04:41 AM   #3
rajeshkmaurya08
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Location: india

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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.
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