Combine vcfs for multi-allelic sites
Hi, I am trying to merge two vcfs (which are created using same pipeline and references) using combinevariants tool.
The variant I am intereted in is indel and has multi-alleles. From one vcf file, this site has five different alleles (ref CAAA, alt C CA CAA CAAAA). And from the second vcf fle, it has three different alleles (ref CAA, alt C CA).
When these two files are merged, it has five alleles. The problem is that samles from the second file have different genotypes compared to the original file. Their alleles were C CA or CAA in the original file, but they were changed to CAA CAAA CAAAA.
When I loaded these two files separately with "variant tool", it seems that they carry CAA CAAA CAAAA, which means CombineVariants worked well.
I wonder why the original file shows different alleles.