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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Genome Mask Files
Genome STRiP makes use of mask files that identify portions of the reference
sequence that are not reliably alignable.
Genome mask files are fasta files with the same number of sequences and of the
same length as the reference sequence. In a genome mask file, a base position
is marked with a 0 if it is reliably alignable and 1 if it is not. Each genome
mask file is specific to the reference sequence and to the parameters used to
The current generation of mask files are based on fixed read lengths. A base
is assigned a 0 if an N base sequence centered on this read is unique within
the reference genome. You should use a genome mask with a value of N that
corresponds to the read lengths of your input data set. For example, if you
have data that is a uniform set of Illumina paired-end data with 101bp reads,
then you should use (or generate) a genome mask with a read length of 101. If
your data is a mixture of read lengths, one viable strategy is to use a
"lowest common denominator" approach and use a mask length corresponding to
the shortest reads in your input data set. Using the smallest read length will
cause a small additional fraction of the genome to be marked inaccessible, but
will give the best specificity. Alternatively, you can use a larger N, which
should modestly improve sensitivity at the cost of a modest increase in false
discovery rate and a modest decrease in genotyping accuracy.
Some precomputed mask files for a variety of reference sequences and read
lengths are available at ftp://ftp.broadinstitute.org/pub/svtoolkit/svmasks.
3. Generating your own genome mask
The ComputeGenomeMask command line utility is available
to generate genome mask files, but queue scripts to automate the process have
not been written. A reasonable strategy is to compute the genome mask in
parallel chromsome-by-chromosome and then merge the resulting fasta files into
a final genome-wide mask file.
4. Planned Enhancements
The implementation of mask files will be replaced in a future release.
Mask files are being converted from textual fasta files to binary files and
are being enhanced to better support input data sets with multiple read
lengths (so the use of a "lowest common denominator" strategy will no longer