For parallel processing I split the original fastq files into smaller ones (1000000 reads per file) and performed trimming, alignment, post processing, etc. Now I want to merge them (487 files) for base recalibration and SNP calling. I'm finding that samtools merge is extremely slow, and I've looked up ways to improve efficiency on github (like this one https://github.com/samtools/samtools/issues/203). They claimed that they were able to merge 4500 bam files in less than 3 hours after making this code change, although it's true they didn't specify the size of each bam file. For me, each bam file is about 1.8 MB, and it is still not complete even after 30 hours. I was wondering if something is wrong or if I there is another tool that's faster? Thanks!