A GRanges object containing unique regions with genomic mappability score equal to 1. Selected from DUKE uniqueness mappability track of the UCSC genome browser (hg19, wgEncodeCrgMapabilityAlign50mer table).
Code used to retrieve these regions:
curl http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeCrgMapabilityAlign50mer.bw > wgEncodeCrgMapabilityAlign50mer.bw
./bigWigToBedGraph wgEncodeCrgMapabilityAlign50mer.bw wgEncodeCrgMapabilityAlign50mer.bedgraph
awk ' if ($4 >= 1) print $0 ' wgEncodeCrgMapabilityAlign50mer.bedgraph > wgEncodeCrgMapabilityAlign50mer_UNIQUEregions.bedgraph
Used as 'RegionsToKeep' within the QCfilter function so that variants NOT overlapping these regions will be removed.
A GRanges object of 9831690 ranges.
These regions are not applicable to longer reads (> 50bp).
Ines de Santiago [email protected]
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