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Make GATK tool to sort non-VCF reference-ordered files #2197
New tool for generating properly sorted non-VCF reference-ordered files (i.e. refseq).
There was a script that did this for refseq files, but it was deprecated. Users have asked for the script, but it is best to make a new tool to do this instead of providing an external script. For example, we may have refseq files where entries are not ordered by reference position. This tool should re-order entries according to a sequence dictionary, like what Picard SortVcf does for VCFs, but for generic ROD formats.
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