Hi,
I'm quite new to SNP analysis and I there's something I think should be simple to do but I cannot find any existing programs to help me. I want to find all the SNPs that are candidates for differences between two bacterial strains. I've tried programs like Harvest Suite, which is nice for viewing the SNPs but it can't output what I need: i.e. a list of SNPs that are fixed and different between the groups (akin to private alleles in a classical mapping). I could view them all manually, but that seems silly when it should be a simple thing to automatically output.
I'm hoping I don't have to write a script to parse the VCF files.. I hate those files..
Thanks for any help,
Susan
I'm quite new to SNP analysis and I there's something I think should be simple to do but I cannot find any existing programs to help me. I want to find all the SNPs that are candidates for differences between two bacterial strains. I've tried programs like Harvest Suite, which is nice for viewing the SNPs but it can't output what I need: i.e. a list of SNPs that are fixed and different between the groups (akin to private alleles in a classical mapping). I could view them all manually, but that seems silly when it should be a simple thing to automatically output.
I'm hoping I don't have to write a script to parse the VCF files.. I hate those files..
Thanks for any help,
Susan
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