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Add emit original BQ option when using BQSR #26

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mfoll opened this issue Apr 23, 2020 · 0 comments

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mfoll commented Apr 23, 2020

From GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360037055712-ApplyBQSR

Emit original base qualities under the OQ tag
The tool is capable of writing out the original quality scores of each read in the recalibrated output file under the "OQ" tag. By default, this behavior is disabled because emitting original qualities results in a significant increase of the file size. Use this flag to turn on emission of original qualities.

mfoll mentioned this issue

Allow to retrieve original quality scores during BAM -> FASTQ #28

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