Fastest way to use pysam view in order to get the reads in different regions

Question

[MarVi]

Dear all,

I am trying to retrieve all reads in several different regions for several bam files. I am writing my code in python, using the pysam library as follows,

pysam.view("-F0X100", bam_file, region_to_query)

Everything works, but I am concerned about the time it takes to process each bam file. It seems that the I/O takes a long time since I am querying each region at a time.

Would you have any suggestions on how I can speed up the querying of each bam file?

[Jianyu]

Have you tried "bedtools intersect"? I guess you can easily intersect each bam file with the bed file (regions) in parallel by bedtools, then merge the output bam files finally.