Question: Duplicate variants in same position: bcftools
1
gravatar for Mbillah
5 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 • 321 views
ADD COMMENTlink modified 5 months ago by zx87547.8k • written 5 months ago by Mbillah110

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

ADD REPLYlink written 5 months ago by finswimmer11k
1
gravatar for Pierre Lindenbaum
5 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k 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 5 months ago by Pierre Lindenbaum121k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 925 users visited in the last hour