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Updates to the pangenome pipeline: - Output a deduped CRAM file - Reduce kmc default memory to 58g - Remove the indel realignment step - Add the `IndelLeftAlignReadTransform` read filter - Update the `estimate_ploidy.py` script to handle multiple input bams
* Use the new `.hdr` functionality to strip contig prefixes. * Use `--into-paths <paths.dict>` argument in `vg surject` instead of `--into-ref GRCh38` to control the contig order.
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Initial implementation of a pangenome pipeline.