I have SNVs from the patients. And I also have the ATAC-seq data from the same patient. Now I am looking for extracting allele specific reads using the SNV positions.
I was wondering if there is any tool available for this purpose. Can we do this using samtools?
Any suggestions will be highly appreciated?
Any of the normal allele-specific tools (e.g., lapels and then suspenders) should work. Not that you'll need to randomly assign each heterozygous allele to one genome. The results will likely be better if you try to phase the variants first.