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Reanalyzing data with a newer version of GATK


I have a total 120 exomes that have been single-sample called using GATK version 1.4.15 and hard filters. I'm now planning to perform multi-sample calling combined with VQSR using the newest version of GATK. I suppose it is recommended to repeat not only variant calling but also indel realignment and base recalibration using the latest version of GATK? If I better repeat those steps as well, I'm wondering whether I could use the uncompressed BAM file that I got from base recalibration using old version of GATK as an input for the new indel realignment. For practical reasons it would be convenient for me to use that file as an input. Or should I revert the BAM to fastq and redo also mapping and duplicate marking?

Best, Mikko

Best Answer


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