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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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GATK Indel Realigner #62

Closed ArashBayat closed 5 years ago

ArashBayat commented 6 years ago

Hi, I know that GATK HaplotypeCaller does not require Indel Realignment as it locally re-assemble the genome. However, Pilon does not seem to have such re-assembling step.

Does the Pilon have indel realignment itself?

Could running GATK indel realigner prior to Pilon enhance the polishing quality of Pilon?

Thanks

orangeSi commented 6 years ago

pilon maybe has local assembly： --fix fixlist A comma-separated list of categories of issues to try to fix: "snps": try to fix individual base errors; "indels": try to fix small indels; "gaps": try to fill gaps; "local": try to detect and fix local misassemblies; "all": all of the above (default);