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tseemann / ekidna

Assembly based core genome SNP alignments for bacteria
GNU General Public License v3.0
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Use CIGAR lines to find micro deletions relative to the reference #10

Open tseemann opened 5 years ago

tseemann commented 5 years ago

We currently use the unaligned regions and set them to gaps in the aligement (no coverage).

But the aligned regions could have small INS and DEL in them. Those DEL should be masked off in the respective sample.