I have a BAM file, and a big read list. What I want to do is to remove the reads in the read list from the BAM file. I can transform Bam to Sam file and then use a Python script to remove unwanted reads. And then transform Sam to Bam again. But I am wondering if there is a more efficient way, which I mean faster, easier, and memory-efficient, to achieve this goal?
Any advice is appreciated!