Do you need to sort bam files that you have intersected before with bedtools

Question

[LDT]

Dear all,

the silly question in here. I have sorted and indexed my bam files. After that, I had to use the bedtools to remove alignments in a few regions and I created new bam files.

Do I need to sort the bam files again?

thank you for your time

[Pierre Lindenbaum]

After that, I had to use the bedtools to remove alignments in a few regions

hum... IMHO, the command of choice would be: samtools view -M -L complement.bed -O BAM -o filtered.and.sorted.bam in.bam