This directory contains FASTA files which contain a modified version
of the Build 36.1 finished human genome assembly (hg18,
Mar. 2006). The chromosomal sequences were assembled by the
International Human Genome Project sequencing centers.  The hg18/36.1
assembly was changed to use IUPAC ambiguous nucleotide characters at
each base covered by a stringently filtered subset of single-base
substitutions annotated by dbSNP build 129.  For example, if the
assembly has an 'A' at a position where dbSNP has annotated an A/C/T
substitution SNP, the 'A' is replaced by 'H' in the FASTA file here.  

dbSNP single-base substitutions were excluded from masking in the
following cases:
- UCSC tagged the dbSNP item with any of these exceptions (see also
  hg18.snp129Exceptions and hg18.snp129ExceptionDesc database tables):
  - MultipleAlignments: dbSNP mapped item to multiple locations
  - ObservedMismatch: the reference allele does not appear in the item's
    observed alleles.
  - ObservedWrongFormat: the observed sequence has an unexpected format
    (no instances of this exception were found in snp129)
- dbSNP item class is not "single".
- dbSNP item length is not exactly one base.
- dbSNP item weight is greater than 1.  (lower weight = higher confidence)
The remaining single-base substitutions were used to mask the genomic 
sequence.

Files included in this directory:

chr*.subst.fa.gz - FASTA files with IUPAC characters for substitution SNPs

md5sum.txt - checksums of files in this directory

------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/hg18/bigZips. To download multiple files, use
the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/snp129Mask/ .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/snp129Mask/chr1.subst.fa.gz .

Or with wget, all files:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/snp129Mask/*'
With wget, a single file:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/snp129Mask/chr1.subst.fa.gz' \
        -O chr1.subst.fa.gz

To uncompress the fa.gz files:
    gunzip <file>.fa.gz

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt01-Jul-2008 12:03 2.6K 
[   ]chr1.subst.fa.gz30-Jun-2008 15:43 72M 
[   ]chr2.subst.fa.gz30-Jun-2008 15:45 76M 
[   ]chr3.subst.fa.gz30-Jun-2008 15:46 62M 
[   ]chr4.subst.fa.gz30-Jun-2008 15:46 60M 
[   ]chr5.subst.fa.gz30-Jun-2008 15:46 57M 
[   ]chr5_h2_hap1.subst.fa.gz30-Jun-2008 15:46 550K 
[   ]chr6.subst.fa.gz30-Jun-2008 15:46 53M 
[   ]chr6_cox_hap1.subst.fa.gz30-Jun-2008 15:47 1.5M 
[   ]chr6_qbl_hap2.subst.fa.gz30-Jun-2008 15:47 1.3M 
[   ]chr7.subst.fa.gz30-Jun-2008 15:47 49M 
[   ]chr8.subst.fa.gz30-Jun-2008 15:47 45M 
[   ]chr9.subst.fa.gz30-Jun-2008 15:47 38M 
[   ]chr10.subst.fa.gz30-Jun-2008 15:43 42M 
[   ]chr11.subst.fa.gz30-Jun-2008 15:44 42M 
[   ]chr12.subst.fa.gz30-Jun-2008 15:44 41M 
[   ]chr13.subst.fa.gz30-Jun-2008 15:44 31M 
[   ]chr14.subst.fa.gz30-Jun-2008 15:44 28M 
[   ]chr15.subst.fa.gz30-Jun-2008 15:44 26M 
[   ]chr16.subst.fa.gz30-Jun-2008 15:44 25M 
[   ]chr17.subst.fa.gz30-Jun-2008 15:45 24M 
[   ]chr18.subst.fa.gz30-Jun-2008 15:45 24M 
[   ]chr19.subst.fa.gz30-Jun-2008 15:45 17M 
[   ]chr20.subst.fa.gz30-Jun-2008 15:45 19M 
[   ]chr21.subst.fa.gz30-Jun-2008 15:45 11M 
[   ]chr22.subst.fa.gz30-Jun-2008 15:46 11M 
[   ]chrM.subst.fa.gz30-Jun-2008 15:47 6.0K 
[   ]chrX.subst.fa.gz30-Jun-2008 15:47 48M 
[   ]chrY.subst.fa.gz30-Jun-2008 15:47 7.9M 
[TXT]md5sum.txt01-Jul-2008 11:47 1.4K 

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