> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/access-quality-control-v1/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/access-quality-control-v1/base-quality-recalibration-scores.md).

# Base Quality Recalibration Scores

Checking for low base quality samples

![](https://2763969089-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M52gq1rRSDQOKMQGEuR%2F-M9Z39Nd7c6cJRknLQBm%2F-M9Z6fe9BQxh8PkX2U03%2FScreen%20Shot%202020-06-11%20at%2012.02.48%20PM.png?alt=media\&token=982d68cf-1e46-47b3-8dc2-545aeb3197bf)

**Theoretical Method**

The sequencer uses the difference in intensity of the fluorescence of the bases to give an estimate of the quality of the base that has been read. The BaseQualityScoreRecalibration (BQSR) tool from GATK recalculates these values based on the empirical error rate of the reads themselves, which is a more accurate estimate of the original quality of the read. 

**Technical Methods**

* Tool Used:
  * GATK BaseQualityScoreRecalibration
  * Picard MeanQualityByCycle
* Input
  * Standard, Uncollapsed Bams
* Output
  * sample\_id.bam.quality\_by\_cycle\_metrics
  * sample\_id.bam.quality\_by\_cycle.pdf

**Interpretations**

It is normal to see a downwards trend in pre and post-recalibration base quality towards the ends of the reads. Average post-recalibration quality scores should be above 20. Spikes in quality may be indicative of a sequencer artifact.