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GATK4 vs GATK3 output file compatability

Dear GATK team,

I have applied GATK3 to hundreds of genomes to obtain BQSR tables via the output of the "BaseRecalibrator" command. Only the BQSR table is saved - no other intermediate file is kept

I would like to upgrade to GATK4.

This GATK4 FAQ page cautions about mixing GATK versions for different intermediate steps of the pipeline. Does this apply to the formatting of the final output files produced by GATK3 vs GATK4?

In particular:

1] Is the format of the BQSR table produced by GATK3 vs GATK4 identical?
2] Can BQSR tables produced by GATK3 be used by GATK4 (via "ApplyBQSR") ?
3] Can BQSR tables produced by GATK4 be used b GATK3 (via "PrintReads") ?
4] Is the BQSR table format subject to potentially pipeline-breaking version-to-version changes in the same way that the GATK tools are ?

Thank you,


Best Answer


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