How to convert genome coordinates from two assemblies

[TuA]

Hi!

I’m working with two closely related species ( < 1 MY) and got a reference genome for both of them. I re-sequenced several individuals per species and mapped the reads to the reference genome of the particular species. Now, I would like to look at SNPs between and within the species. For this, I obviously need to have the same genome coordinates for the SNP positions. Does anyone have a good advice how the convert the coordinates? My main concerns are how to deal with indels and how I could still be able to use additional available data of one of the species such as genome annotation.

Your help is greatly appreciated!

[simonandrews]

You should look at the liftOver tool from UCSC which can be used to covert between different coordinate systems. You can create a set of 'chain' files which allow you to convert between coordinates in your different assemblies. The matching is based on either blat (if the species are close enough for a DNA level comparison) or blastz for more distant relationships.

[TuA]

Thanks Simon for your helpful post. It seems to be pretty time intense to create these liftOver chain files. Do you have any experience on the accuracy, i.e. how well the coordinates can be transformed (blat performance)?

Many thanks

[simonandrews]

Thanks Simon for your helpful post. It seems to be pretty time intense to create these liftOver chain files. Do you have any experience on the accuracy, i.e. how well the coordinates can be transformed (blat performance)?

The liftOver chains might take a long time to calculate, but once you have them the speed with which coordinates can be transformed is blazingly quick. I guess the efficiency of the conversion will depend on the degree of identity between your genomes. We mostly use the system for converting between different assemblies of the same genome, and it's very accurate and quick there. If your two genomes are reasonably high identity then you should have no problem.

[TuA]

Thanks for your help! I'll give it a try...

[liguow]

CrossMap

CrossMap is a program for convenient conversion of genome coordinates between assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

http://crossmap.sourceforge.net/