Liftover Bam File

Question

[dfernan]

Hi,

I have a sam file of reads alignment to genome assembly X, and I would like to liftover this Sam File to genome assembly Y, is that possible? Is there any software that can do that? Note that I'd also like to take care of the new CIGARs since the CIGAR field with respect to genome assembly X will be different from the CIGAR field with respect to genome assembly Y. I have chain files that connect the two assemblies.

Please let me know if anyone knows of such software.

Answer 1

[Chris Miller]

This is a bad idea. Since the genome assembly that the reads were mapped to are different, you really need to realign your data. There will undoubtedly be many places where reads map to different places than where liftover would place them, due to the differences between the assemblies. Convert the bam back to a fastq with picard, then redo the mapping with the aligner of your choice.

[dfernan]

@Chris Miller, thanks, but what happens if you know that your reads were generated from genome X instead of the reference genome? Let us say I have two mouse strains, and I do an RNA-Seq experiment with strain X - I should map the reads to strain X, and not to the reference genome. Now the question is why would I want to lift over the bam? this is odd but in my case I need to do it because I am using downstream tools that use reference genomes and not "personalized" genomes.

Answer 2

[microfuge]

CrossMap says can do that http://crossmap.sourceforge.net/