extract reference and query coordinate from bam or sam file
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5 months ago
LMoon • 0

Dear All: I generate a sam file based on the command minimap2 -ax asm20 --cs ref.fa que.fa > out.sam. Now, I want to convert some reference coordinates to query. In other words, similarly to LiftOver, are there some methods that could accurately liftover the reference coordinates to query based on bam or sam files? Thanks!

sam bam • 210 views
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It's not clear to me. Give us an example please.

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For example, I got a sam file after aligning the Chimpanzee assembly to the Human assembly. Now, could I get the Chimpanzee coordinate which matches the Human coordinate chr1:1000-2000 based on the sam or bam file? I know that LiftOver could do similar things based on the command liftover human_coordinate.bed chainfile chimp_coordinate.bed unlift, but there is no chainfile that meets my requirements. So, I want to know if there is a method that could do this?