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There is likely a sinple answer to this, but it's evading me.
I am comparing crosses of 2 wellcome trust mouse strains, PWK and WSB. I need to be able to compare reads on specific SNP positions between these two, but they are mapped to their respective references. How can I create a liftover of the genomic coordinates from one reference to the other? The references are publically available as FASTA and bam files.
I am comparing crosses of 2 wellcome trust mouse strains, PWK and WSB. I need to be able to compare reads on specific SNP positions between these two, but they are mapped to their respective references. How can I create a liftover of the genomic coordinates from one reference to the other? The references are publically available as FASTA and bam files.