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  • anna_vt
    Junior Member
    • Jun 2009
    • 5
    #1

    Liftover bam from custom amplicon to hg19

    Hi,

    I have been aligning sequences to a small subset of hg19 as the project is a custom amplicon.
    Is there any tool for converting the bam files aligned to the custom genome to the full hg19?

    I guess I could create a custom liftover chain file and then use crossmap to liftover.
    Has anyone else done this or similar?

    Cheers
    Tags: bam, custom amplicon, liftover
  • wdecoster
    Member
    • Oct 2015
    • 97
    #2
    The least biased and most correct way would be to repeat the mapping to the full genome. As far as I know, it's not advisable to map to a small subset of the genome since you might be "forcing" the aligner to chose the "best" mapping site which may not be the correct one.

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