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This is a simple program to search for L1Hs insertions in long-read data. Inserted sequences (currently hard-wired) at least 500bp are compared with the L1HS reference sequence as well as flanking reference sequences. A summary of both alignments as well as 5' and 3' TSDs are written for each insertion that aligns with at least 90% identity to L1HS.

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Scan a bam file for l1 insertions.

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