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Merging adjavent SNPs into MNPs.
I have many adjacent SNPs in my VCF that I need to merge into MNP. These SNPs can be homozygous or heterozygous.
chr1 889158 rs13303056 G C
chr1 889159 rs13302945 A C
The two SNPs above need to be turned into the MNP below:
chr1 889158 . GA CC
I tried the option --mergeVariantsViaLD in HaplotypeCaller but as mentioned in other posts, it didn't really work.
What are my options for merging?