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epam / fonda

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Apache License 2.0
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Add gatk recalibration to ABRA aligner in PostAlignment #190

Closed syansanofi closed 3 years ago

syansanofi commented 3 years ago

Issue Regardless of which realigner is used, read quality recalibration must be added. Currently ABRA realigner does not include recal.

https://github.com/epam/fonda/blob/72759b47b5bb92c43d496907fb041c96837be49c/src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java#L81-L94