This directory contains FASTA files which contain a modified version
of the Genome Reference Consortium human genome build 37 (hg19, Feb. 2009). 
The chromosomal sequences were assembled by the International Human 
Genome Project sequencing centers.  The hg19/GRCh37 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 137.  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 the
  exceptions field of the hg19.snp137 database table as well as the
  hg19.snp137ExceptionDesc table):
  - 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
- 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/hg19/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/hg19/snp137Mask/ .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp137Mask/chr1.subst.fa.gz .

Or with wget, all files:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp137Mask/*'
With wget, a single file:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp137Mask/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.txt12-Jul-2012 07:15 2.6K 
[   ]chr1.subst.fa.gz11-Jul-2012 15:41 75M 
[   ]chr2.subst.fa.gz11-Jul-2012 15:46 79M 
[   ]chr3.subst.fa.gz11-Jul-2012 15:48 65M 
[   ]chr4.subst.fa.gz11-Jul-2012 15:49 63M 
[   ]chr4_ctg9_hap1.subst.fa.gz11-Jul-2012 15:49 196K 
[   ]chr5.subst.fa.gz11-Jul-2012 15:50 59M 
[   ]chr6.subst.fa.gz11-Jul-2012 15:50 56M 
[   ]chr6_apd_hap1.subst.fa.gz11-Jul-2012 15:50 809K 
[   ]chr6_cox_hap2.subst.fa.gz11-Jul-2012 15:50 1.6M 
[   ]chr6_dbb_hap3.subst.fa.gz11-Jul-2012 15:50 1.4M 
[   ]chr6_mann_hap4.subst.fa.gz11-Jul-2012 15:50 1.4M 
[   ]chr6_mcf_hap5.subst.fa.gz11-Jul-2012 15:50 1.3M 
[   ]chr6_qbl_hap6.subst.fa.gz11-Jul-2012 15:50 1.4M 
[   ]chr6_ssto_hap7.subst.fa.gz11-Jul-2012 15:51 1.4M 
[   ]chr7.subst.fa.gz11-Jul-2012 15:52 52M 
[   ]chr8.subst.fa.gz11-Jul-2012 15:52 48M 
[   ]chr9.subst.fa.gz11-Jul-2012 15:52 40M 
[   ]chr10.subst.fa.gz11-Jul-2012 15:42 44M 
[   ]chr11.subst.fa.gz11-Jul-2012 15:42 44M 
[   ]chr12.subst.fa.gz11-Jul-2012 15:42 43M 
[   ]chr13.subst.fa.gz11-Jul-2012 15:43 32M 
[   ]chr14.subst.fa.gz11-Jul-2012 15:43 29M 
[   ]chr15.subst.fa.gz11-Jul-2012 15:43 27M 
[   ]chr16.subst.fa.gz11-Jul-2012 15:43 26M 
[   ]chr17.subst.fa.gz11-Jul-2012 15:43 26M 
[   ]chr17_ctg5_hap1.subst.fa.gz11-Jul-2012 15:44 512K 
[   ]chr17_gl000205_random.subst.fa.gz11-Jul-2012 15:44 53K 
[   ]chr18.subst.fa.gz11-Jul-2012 15:45 25M 
[   ]chr19.subst.fa.gz11-Jul-2012 15:46 18M 
[   ]chr20.subst.fa.gz11-Jul-2012 15:46 20M 
[   ]chr21.subst.fa.gz11-Jul-2012 15:47 12M 
[   ]chr22.subst.fa.gz11-Jul-2012 15:48 12M 
[   ]chrM.subst.fa.gz11-Jul-2012 15:52 6.2K 
[   ]chrX.subst.fa.gz11-Jul-2012 15:52 49M 
[   ]chrY.subst.fa.gz11-Jul-2012 15:52 8.1M 
[TXT]md5sum.txt12-Jul-2012 07:13 1.9K 

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