Question: Duplicate variants in same position: bcftools
1
gravatar for Mbillah
21 months ago by
Mbillah110
China
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 • 1.3k views
ADD COMMENTlink modified 3 months ago by sami20 • written 21 months ago by Mbillah110

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

ADD REPLYlink written 21 months ago by finswimmer14k

POS-----VARIANTS---------REF---------------------Allele Variations

99162-----DEL/MNP---TCGGTGTGCGCGG-----TCGG

99166-----SNP-------------------T-------------------------------C

I have on my VCF: DELETION in position 99162 and SNP in position 99166.

It is impossible to have deletion in 99162 and snp in 99166 in the same time. How can i explain that ?? Should i keep snp or deletion in my vcf? Please help me.

Thank you for your answer.

ADD REPLYlink written 3 months ago by sami20

You've already asked a question. Please do not spam other threads - this behavior will lead to your account being suspended.

Plus, this is not an answer. I'm moving it to a comment for now, but will be deleting any similar posts in the future.

ADD REPLYlink modified 3 months ago • written 3 months ago by RamRS30k

@RamRS don't let me deactivate my account and leave this group forever !

ADD REPLYlink written 3 months ago by sami20

Please stop adding answers. Use Add Comment or Add Reply as appropriate instead.

ADD REPLYlink written 3 months ago by RamRS30k
1
gravatar for Pierre Lindenbaum
21 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k 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 21 months ago by Pierre Lindenbaum131k
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: 1598 users visited in the last hour