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 141. 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.snp141 database table as well as the hg19.snp141ExceptionDesc 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/snp141Mask/ . For a single file, e.g. chr1.subst.fa.gz rsync -avzP \ rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp141Mask/chr1.subst.fa.gz . Or with wget, all files: wget --timestamping \ 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp141Mask/*' With wget, a single file: wget --timestamping \ 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp141Mask/chr1.subst.fa.gz' \ -O chr1.subst.fa.gz To uncompress the fa.gz files: gunzip <file>.fa.gz
Name Last modified Size Description
Parent Directory - chr1.subst.fa.gz 2014-08-29 16:24 75M chr2.subst.fa.gz 2014-08-29 16:25 80M chr3.subst.fa.gz 2014-08-29 16:25 66M chr4.subst.fa.gz 2014-08-29 16:25 63M chr5.subst.fa.gz 2014-08-29 16:25 60M chr6.subst.fa.gz 2014-08-29 16:26 56M chr7.subst.fa.gz 2014-08-29 16:26 52M chr8.subst.fa.gz 2014-08-29 16:26 48M chr9.subst.fa.gz 2014-08-29 16:26 40M chr10.subst.fa.gz 2014-08-29 16:24 44M chr11.subst.fa.gz 2014-08-29 16:24 44M chr12.subst.fa.gz 2014-08-29 16:24 44M chr13.subst.fa.gz 2014-08-29 16:24 32M chr14.subst.fa.gz 2014-08-29 16:24 30M chr15.subst.fa.gz 2014-08-29 16:24 27M chr16.subst.fa.gz 2014-08-29 16:24 27M chr17.subst.fa.gz 2014-08-29 16:25 26M chr18.subst.fa.gz 2014-08-29 16:25 25M chr19.subst.fa.gz 2014-08-29 16:25 18M chr20.subst.fa.gz 2014-08-29 16:25 20M chr21.subst.fa.gz 2014-08-29 16:25 12M chr22.subst.fa.gz 2014-08-29 16:25 12M chrM.subst.fa.gz 2014-08-29 16:26 6.4K chrX.subst.fa.gz 2014-08-29 16:26 50M chrY.subst.fa.gz 2014-08-29 16:26 8.1M md5sum.txt 2014-08-29 17:02 1.3K