Duplicate variants in same position: bcftools

Question

[Mbillah]

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

[finswimmer]

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

[sami]

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.

[Ram]

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.

[sami]

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

[Ram]

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

Answer 1

[Pierre Lindenbaum]

How can I handle this situation?

try to use bcftools norm

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