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Full masked genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)

Bioconductor version: Release (3.19)

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

Author: The Bioconductor Dev Team

Maintainer: Bioconductor Package Maintainer <maintainer at>

Citation (from within R, enter citation("BSgenome.Hsapiens.UCSC.hg19.masked")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews AnnotationData, BSgenome, Genetics, Homo_sapiens
Version 1.3.993
License Artistic-2.0
Depends R (>= 3.5.0), BSgenome(>= 1.54.0), BSgenome.Hsapiens.UCSC.hg19
Imports BSgenome, BSgenome.Hsapiens.UCSC.hg19
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Depends On Me
Imports Me
Suggests Me CNVfilteR, CopyNumberPlots, karyoploteR, r3Cseq, regioneR, RSVSim, gkmSVM
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Follow Installation instructions to use this package in your R session.

Source Package BSgenome.Hsapiens.UCSC.hg19.masked_1.3.993.tar.gz
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