Variant Discovery in High-Throughput Sequencing Data
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery
and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
When looking at the GATK processing for variant discovery WDL script, I noticed that the Broad team use the parameter --use-original-qualities in both of the BQSR steps. Why is this the case? Wouldn't we want to keep the new recalibrated base qualities in most cases?