Problems of common variants substraction after using CombineVariants

mglyon1mglyon1 FranceMember

Hello everybody,

I am currently working on WGS data from C. elegans genome resequencing.
I am trying to improve the substraction of common variants shared by multiple mutant strains.
After in silico complementation test, I noticed that some common variants (same mutation at the same position in the same gene) were still remaining in the output vcf post substraction.
I have thus 2 questions :
-How CombineVariants does exactly the selection of the common variants ? Which columns/information in the vcf does it take into account ?
-Are there any parameter that I can modulate to remove these remaining common variants, by looking at the column where the DNA change with the position are indicated, for instance ?

Thanks in advance for any help !

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    It depends how you're doing this in practice as there are several ways to achieve the same result. Can you please post the commands you are using and some sample output, including some variant records that you believe should be removed but are not?
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