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Problems of common variants substraction after using CombineVariants
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 !