Hello, Tara. According to one of our engineers, the 1000 Genomes Project is the best source for NA12878 variants since NA12878 was one of the deeply-sequenced trio individuals in the pilot. Those files are available as VCF files from http://www.1000genomes.org/data.
Regarding your coordinate question, what is your goal in using the coordinate ranges contained in your files? A simple script can easily parse the file and adjust the formatting of your coordinates. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Tara C Sent: Wednesday, June 20, 2012 2:49 AM To: [email protected] Subject: [Genome] How to extract SNPs info (NA12878) from UCSC browser? Hi, May I know how I could extract the SNPs information of NA12878 from UCSC browser? I tried to download the SNPs informattion using Galaxy, I managed to download but the genomic coordinates become something like "chr3 60595 60596 A/C ", and not " chr3:32207307-32210207", how do I match the coordinates to a format like chr3:32207307-32210207? Thank you very much Best regards Tara C _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
