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Does the best practice pipeline for pre-data processing output a merged BAM file?

minimaxminimax Member
edited May 20 in Ask the GATK team

I'm using the GATK4 best practice pipeline for pre-data processing. I have several questions and would like to confirm:

  1. The final output is a merged BAM file, right? All the input per-sample BAM files are merged during MarkDuplicates and are processed together ever since.

  2. It seems that I can use SplitSam on the final output to extract the BAM files for each sample, is this correct?

  3. In the accompanying .json file, the sample_name is NA12878. Are there any special reasons for choosing this name? Or can it be any name?

Also following the 1st question, why all the input BAM files are merged? Are there any special reasons for doing so? For the dataset I'm analyzing, each BAM is about 15GB, and I have 200 such files, if they are merged together it will be 3000GB = 3TB. Although I'm using a server, still it will be very difficult to process such a huge file (if such a huge file could be supported)! Besides, since they are merged, we will not be able to have parallel computing, and the computing time will be longer.

Thank you very much for your help!

Best Answer

Answers

  • minimaxminimax Member

    @SChaluvadi , thanks for your reply!

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