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!
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!
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