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Extract variant fragments (version 0.5.25)

Extract variants will find soft-clipped alignments and alignments with insertions, and, if the inserted sequence aligns with the selected reference, write out a the alignment, but clip the aligned portion of the read to a single N and will add 2 tags, AR and AD to the alignment. The AR tag will list the contig, the AD tag contains detailed information on how the insert/clipped sequence aligned against the selected reference.