Bcftools consensus when reference is a deletion
1
0
Entering edit mode
12 weeks ago
selplat21 ▴ 20

Hello,

I am trying to call a consensus on a VCF file like so:

bcftools consensus species.vcf.gz -f Reference.fasta --absent N > Consensus.fasta

Error: The site SUPER_1:173197 overlaps with another variant, skipping...

I looked at this site and included the previous site

SUPER_1 173196  .       AT      A      
SUPER_1 173197  .       T       A   

How would you recommend dealing with this overlapping variant error:

I have tried bcftools norm -m +any, but this does not modify these types of sites in the VCF, so am unsure how to merge these types of entries or call a consensus without these overlapping variant errors.

consensus vcf • 224 views
ADD COMMENT

Login before adding your answer.

Traffic: 2669 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6