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Old 10-31-2016, 03:16 AM   #1
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Location: London

Join Date: Jun 2009
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Default Liftover bam from custom amplicon to hg19


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?

anna_vt is offline   Reply With Quote
Old 10-31-2016, 12:23 PM   #2
Location: Antwerp, Belgium

Join Date: Oct 2015
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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.
wdecoster is offline   Reply With Quote

bam, custom amplicon, liftover

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