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A question about the database bed file：cn2_mask_g1k_v37.mask.bed
I just want to confirm that if the file cn2_mask_g1k_v37.mask.bed( which come from the link [ftp://ftp.broadinstitute.org/pub/svtoolkit/cn2masks/cn2_mask_g1k_v37.mask.bed] can serve as segmental_duplication_file specified by parameter "--segmental-duplication-track" of the tools AnnotateIntervals?
Asking because I use this as the segmental duplication files, then I found that, some filtered intervals are not repeat regions,like this two filtered intervals:
chr12 25378298 25378957 0.313636 1.000000 0.734848
chr12 25397958 25398579 0.337621 1.000000 1.000000