Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.
Convert GATK style interval list file to a BED file
Is there an existing tool to convert a GATK formatted interval list file (such as the one outputted by FindCoveredIntervals) to a BED file?
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