EIR_Implementation

The following table and figure together illustrate differing representations and how they may be resolved using proper implementation of EIR.

chr6    32584700    G    1    .    0    .    .    chr6    32584700    .    G    G    .    PASS    SNP
chr6    32584701    G    1    .    0    .    .    chr6    32584701    .    G    G    .    PASS    SNP
chr6    32584702    A    1    .    0    .    .    chr6    32584702    .    A    A    .    PASS    SNP
chr6    32584703    G    1    .+6CCTCCA    0    .    .    chr6    32584703    .    G    G    .    PASS    SNP
chr6    32584704    C    1    .    0    .    .    chr6    32584704    .    C    C    .    PASS    SNP
chr6    32584705    C    1    .    0    .    .    chr6    32584705    .    C    CTCCACC    .    PASS    INS
chr6    32584706    C    1    .    0    .    .    chr6    32584706    .    C    C    .    PASS    SNP
chr6    32584707    C    1    G    0    .    .    chr6    32584707    .    C    C    .    PASS    SNP
chr6    32584708    A    1    .    0    .    .    chr6    32584708    .    A    A    .    PASS    SNP

Calculating the equivalent insertion and deletion region demonstrating how the first (query) from the table above can be rotated into the second (target). For a given reference sequence (or snippet) an insertion or deletion pattern can be rotated leftward or rightward as described in the algorithm above. In this case the beginning rotation is possible because the first letter in the insertion pattern matches the reference (C:C) whereby the insertion is moved right one position and the pattern is rotated (CCTCCA --> CTCCAC). In other words the first letter of the insertion 'C' replaces the reference 'C', which is appended to the pattern. The next rotation is possible because, again, the first letter in the (rotated) insertion pattern matches the reference (C:C). The insertion is moved right one more position and the pattern is rotated (CTCCAC --> TCCACC). The next rotation is not possible because the first letter in the insertion pattern does not match the reference (T:C) so the algorithm exits normally and the equivalent region for this insertion with respect to the reference is chr6:32584703-32584705.