Description of the bug

Currently, Sarek produces BAM files for variant calling through the GATK best-practices, including recalibration (default).

For DeepVariant, this is discouraged, as stated by the developers:

https://github.com/google/deepvariant/blob/r1.4/docs/trio-merge-case-study.md

It is recommended to use BAM files with original quality scores. In the case that BAM files went through recalibration, optional DV flags can be used in order to use original scores: --parse_sam_aux_fields, --use_original_quality_scores.

While recalibration can be disabled globally within Sarek, this would potentially have a negative impact on e.g. the GATK subworkflow, where recalibration is still considered to be useful (not sure it really is...).

Solution:

1. Easy: Have an optional parameter in the Deepvariant module that sets the above flags if recalibration was performed
2. Slighty less easy: Emit both deduped and deduped+recalibrated BAM/CRAM files after the GATK BP alignment/deduping and pass them to the appropriate subworkflows, i.e. GATK gets the recal BAM file, all other subworkflows get the non-recalibrated BAM. This might be the better choice in the long-term, depending on what the effect of recalibration is on other callers/tools (largely unexplored, I think).

Command used and terminal output

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Relevant files

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System information

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