Hello,
-I am seeking your expertise to identify a command-line tool or package that can be used to phase my VCF file ( to convert genotype representations from unphased (using "/") to phased (using "|")). Could you recommend any suitable tools or methodologies for this purpose ?
Before I moove to the second question, I'd like to clarify that my reference genome is just a gene sequence.
-So, once I have the phased VCF, I would like to analyze the number of reads that contain multiple variants (haplotypes). In other words, I need to determine the count of reads that simultaneously harbor two or more mutations (variants). (I am focusing on just 10 specific variants for this analysis). Could you advise on how to extract and calculate this information?
Thank you for your assistance.
