Split BAM file into two subsamples


I want to create two random subsamples from a BAM file. I don't want to just do "samtools view -s 0.5" twice because I want to put half of the reads into one file and half in the other, without replacement. Is there an easy way to do this? I've considered using samtools to output the alignments in SAM format and pipe to the shuf and split commands, I think I'd need to do some extra things to keep the paired-end reads together. Anyone have any ideas?



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