Question: How to subtract out wildtype variants, and what is it?
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gravatar for tmrhyd
6 weeks ago by
tmrhyd0
tmrhyd0 wrote:

I have Bam files, sorted and indexed, and VCF files, and was told that I need to subtract the wildtype variants out of my files, and to use VCFtools or Freebayes.

What is subtracting out the wildtype variants? How do I do it? Since I have VCF files is it already done?

Thank you all so much!!

snp assembly genome • 106 views
ADD COMMENTlink written 6 weeks ago by tmrhyd0

Is this human data or something else?

ADD REPLYlink written 6 weeks ago by genomax70k

Perhaps I need more information, but the current question doesn't make sense. "Wildtype" is commonly used for alleles which are the same as the reference genome. So, therefore, a wildtype allele is not a variant.

You were told to use VCFtools or Freebayes, but those are two very different tools. VCFtools is for filtering and manipulation of vcf files (a better tool would be bcftools) and Freebayes is a variant caller - but you already have the vcf files, so you don't need a variant caller anymore.

What is the aim of the study?

I think you should talk again to the one who told you to do this, and make sure you understand what should be done.

ADD REPLYlink written 6 weeks ago by WouterDeCoster40k
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