Hello Xinwei, Unfortunately, the code that handles the realignments is not a stand-alone package; it is part of the code that generates the SNP details pages generated by clicking on an individual SNP.
However, you may be able to use BLAT (http://genome.ucsc.edu/cgi-bin/hgBlat?command=start) to generate alignments in PSL format, which you can then upload as a custom track. I hope this proves to be useful to you. Please contact us again if you have further questions. Best, Antonio Coelho UCSC Genome Bioinformatics Group She, Xinwei wrote: > Hi: > > UCSC genome browser realigned dbSNP flanking sequence to obtain the > coordinates of the SNPs. There are some new SNPs that I'd like to map to > the genome and put into a custom track. Is it possible to obtain the SNP > realignment package or pipeline so that I can do it on our local > machine? Thanks. > > Xinwei > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
