Hello, I am trying to extract all human SNPs with big indels in a batch. I am interested in the sequences with and without the indels plus the flanking regions. I want to get for each snp an alignment similar to that appear in each snp page.
I took a look here http://www.soe.ucsc.edu/pipermail/genome/2007- January/012650.html but I have few questions: (a) Here is the approach I start with. I try to treat the insertion/ deletions/in-del in snp128 separately. First I get the sequence and its flanking in the reference genome and then I delete/insert the bases in the right places according to the snp table. Is there a better way to get both sequences for each snp (the reference and the snp) in a batch? (b) Is the information about which variant is the ancestral one available somewhere? Thanks Einat _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
