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possible variant pair. The percentage of matches is given at 3 levels for each
possible variant pair. The percentage of matches is given at 3 levels for each
variant total of both VCF files.
variant total of both VCF files.
The 3 match levels (in order of decreasing strictness) are given as:
The 3 match levels (in order of decreasing strictness) are given as:
Level 1) SRSA - Same Position, same REF and ALT
Level 1) SRSA - Same Position, same REF and ALT
Level 3) DRDA - Same Position, different REF and different ALT
Level 3) DRDA - Same Position, different REF and different ALT
Level 3) DRDNA - Same Position, different REF and different number of ALT
Level 3) DRDNA - Same Position, different REF and different number of ALT
Level 1 represents matches in position and alleles
Level 1 represents matches in position and alleles
Level 2 represents matches in position and reference alleles but different alternate alleles
Level 2 represents matches in position and reference alleles but different alternate alleles
