Resolving of clonotypes
In order for clonotypes to be considered the same, they need to have the same CDR3 sequence and V/D/J/C segments.
Sequencing errors and variability in read quality and length can lead to false positives, see Immune Repertoire Analysis and Merge Immune Repertoire. These can be reduced within one sample using the Merge Immune Repertoire tool, but such false positives can still remain when comparing samples.
If the same clonotype is present in two samples, up to differences due to ambiguous V/D/J/C segments and/or missing C segment, it will be considered as two separate clonotypes, leading to private clonotypes in each sample (see Scatter plot for Clonotype Sample Comparison). To consider them as one clonotype, the Resolve clonotypes with ambiguous segments and/or Resolve clonotypes without C segment can be used.
Resolve clonotypes with ambiguous segments: A clonotype with ambiguous segments may be corrected to have an unambiguous segment, if another sample has the same clonotype with unambiguous segment. Consider a clonotype with ambiguous V segments V-1/V-2 in sample A, and the same clonotype, but with V-1, in sample B. Then the clonotype from sample A is corrected to have V-1. If another sample C is also used, which has the same clonotype, but with V-2, it cannot be determined if V-1 or V-2 is the correct segment for sample A, so the clonotype is not changed.
Resolve clonotypes without C segment: A clonotype without a C segment may be corrected to have a C segment, if another sample has the same clonotype with a C segment. Consider a clonotype without a C segment in sample X, and the same clonotype, but with C-1, in sample Y. Then the clonotype from sample X is corrected to have C-1. If another sample Z is also used, which has the same clonotype, but with C-2, it cannot be determined if C-1 or C-2 is the correct segment for sample X, so the clonotype is not changed.