Question: Duplicate variants in same position: bcftools
gravatar for Mbillah
10 days ago by
Mbillah110 wrote:

I create a vcf file by bcftools mpileup command. But I got the huge number of duplicate variants. Duplicate means it shows different variants in the same position. How can I handle this situation?


chr1 3993567 T A
chr1 3993567 tc t
bcftools vcf • 117 views
ADD COMMENTlink modified 8 days ago by zx87546.5k • written 10 days ago by Mbillah110

Could you please provide the exact command you have used and some complete vcf lines?

ADD REPLYlink written 10 days ago by finswimmer9.9k
gravatar for Pierre Lindenbaum
9 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

How can I handle this situation?

try to use bcftools norm (...) recover multiallelics from multiple rows.

ADD COMMENTlink written 9 days ago by Pierre Lindenbaum116k
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