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Merging SAM files from different runs to run with GATK


I have a trio, that has been sequenced twice in two different centers. One has a 100b read length and the other 101b read length both illumina fastq files. To get a better coverage I want to merge the SAM files and then pass it to GATK to realign, re-calibrate and call variants. I wonder if someone has done that and/or this is the way to do it?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    That shouldn't be a problem, but you don't really need to physically merge the files. You can do the pre-processing (dedup, realign, recal etc) on the separate files, then optionally do realignment on them together, then finally pass them in together as input when you do variant calling. As long as you identify the samples appropriately in the read group information (make sure the SM tag is the same for data that correspond to the same individuals) the GATK will aggregate the data correctly.

  • alirezakjalirezakj Member

    Thanks Geraldine!

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