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 135. 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.snp135 database table as well as the hg19.snp135ExceptionDesc 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 ... - 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/snp135Mask/ . For a single file, e.g. chr1.subst.fa.gz rsync -avzP \ rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp135Mask/chr1.subst.fa.gz . Or with wget, all files: wget --timestamping \ 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp135Mask/*' With wget, a single file: wget --timestamping \ 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp135Mask/chr1.subst.fa.gz' \ -O chr1.subst.fa.gz To uncompress the fa.gz files: gunzip .fa.gz