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<pre>ln -s bin/locuszoom /usr/local/bin/locuszoom</pre>
<pre>ln -s bin/locuszoom /usr/local/bin/locuszoom</pre>
== Sources of SQLite database tables ==
== Sources of information ==
LocusZoom uses various sources of information for annotation, positions, and calculating LD.
For LD:
*[http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/phased HapMap phased haplotypes]
*[http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/phased HapMap phased haplotypes]
*[ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1 1000 Genomes phased haplotypes]
*[ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1 1000 Genomes phased haplotypes]
*[http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP position] via the [http://genome.ucsc.edu UCSC Browser]
*[http://www.ncbi.nlm.nih.gov/RefSeq/ Gene and exon positions] via the [http://genome.ucsc.edu UCSC Browser]. We filtered SNPs that map to more than one location or where no allele matches the reference sequence
For SNP, gene, and exon positions:
*[http://genome.usc.edu Annotation] We used various sources including RefSeq Genes (refFlat), TFBS Conserved (tfbsConsSites), and Conservation (phaseConsElements44wayPlacental)
*[http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP position] via the [http://genome.ucsc.edu UCSC Genome Browser]
*[http://www.ncbi.nlm.nih.gov/RefSeq/ Gene and exon positions] via the [http://genome.ucsc.edu UCSC Genome Browser]. We filtered SNPs that map to more than one location or where no allele matches the reference sequence
For annotation:
*We used various sources including RefSeq Genes (refFlat), TFBS Conserved (tfbsConsSites), and Conservation (phaseConsElements44wayPlacental), all available from the [http://genome.usc.edu UCSC Genome Browser].
*[ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1 Recombination rates from HapMap]
*[ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1 Recombination rates from HapMap]
== Input ==
== Input ==
