Question: Duplicate variants in same position: bcftools
1
gravatar for Mbillah
12 months ago by
Mbillah110
Chittagong
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?

Example:

chr1 3993567 T A
chr1 3993567 tc t
bcftools vcf • 623 views
ADD COMMENTlink modified 12 months ago by zx87549.0k • written 12 months ago by Mbillah110

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

ADD REPLYlink written 12 months ago by finswimmer13k
1
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

How can I handle this situation?

try to use bcftools norm

https://samtools.github.io/bcftools/bcftools.html#norm (...) recover multiallelics from multiple rows.

ADD COMMENTlink written 12 months ago by Pierre Lindenbaum126k
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