Question: Duplicate variants in same position: bcftools
1
gravatar for Mbillah
10 days 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 • 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
1
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

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

ADD COMMENTlink written 9 days ago by Pierre Lindenbaum116k
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