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Joining samples

Dear Support Team,

Thanks for making the GATK 2013 workshop available, those are great videos and answered most of my doubts regarding the use of your pipeline.
I have started analysing my data, but I have some doubts regarding my samples. At the moment I am running a pilot analysis, and I only have 2 samples (two different strains of the same organism). I got the files already demultiplexed from my Illumina sequencer and I have mapped them separately using BWA-MEM. I was planning to analyse them separately, probably using hard filtering.
Should I join the samples at some point? Or should I rather get the multiplexed file (I mean the file before demultiplexing) and then rely on PICARD tools to group the reads separately?

Thanks for your kind attention,
Max

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