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liguowang / CrossMap

CrossMap is a python program to lift over genome coordinates from one genome version to another.
https://crossmap.readthedocs.io/en/latest/
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Can CrossMap lift bam tag values as well? Like NM tag, MD tag #22

Open yangyxt opened 3 years ago

yangyxt commented 3 years ago

The same as the title.

liguowang commented 3 years ago

For regions that are mappable between two assemblies, CrossMap just copied the NM/MD tags. This should not be a problem for most mappable regions. "mappable" means the genomic region from one assembly can be unambiguously mapped to another assembly. However, if the goal is for variant calling, I highly recommend to redo the alignment.

Liguo

On Mon, Nov 9, 2020 at 8:03 PM yxt notifications@github.com wrote:

The same as the title.

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yangyxt commented 3 years ago

Dear @liguowang ,

Thanks for the reply. I'm converting a bam mapped against assembled contig to a bam mapped against ref genome. I cannot directly use raw reads to remap against ref genome since it will completely erase the benefits from local re-assembly.

As to assembled contigs, most of them are mappable to ref assembly(using minimap2), with small editing distance. But the NM and MD tag values can be different given the specific hit by each read. Can CrossMap count that part as well?

liguowang commented 3 years ago

CrossMap only deals with coordinates, not the sequence per se. So CrossMap cannot count even "small editing distance".

Thanks

Liguo

On Mon, Nov 9, 2020 at 8:37 PM yxt notifications@github.com wrote:

Dear @liguowang https://github.com/liguowang ,

Thanks for the reply. I'm converting a bam mapped against assembled contig to a bam mapped against ref genome. I cannot directly use raw reads to remap against ref genome since it will completely erase the benefits from local re-assembly.

As to assembled contigs, most of them are mappable to ref assembly(using minimap2), with small editing distance. But the NM and MD tag values can be different given the specific hit by each read. Can CrossMap count that part as well?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/liguowang/CrossMap/issues/22#issuecomment-724411604, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACN443QY5MCGEIKFX6DSM73SPCRNBANCNFSM4TQCLCLA .