Trim alignment from .sam file based on a specific tab-delimiter .bed file

Question

[khanhlpbao]

Hi, I have seen multiple ways to trim out alignment from .bam file based on a blacklist .bed file. However, I want to trim alignments directly from .sam file based on the blacklist .bed file I already has. Does anyway to me to do this? Thank you very much

[Pierre Lindenbaum]

However, I want to trim alignments directly from .sam file based on the blacklist .bed file I already has

so, what's wrong with the multiple methods you saw ?

[khanhlpbao]

I just don't want to convert the sam to bam to trim alignments and then reconvert it to sam. The process is time-consuming and cost a lot of memory on hard drive

[Pierre Lindenbaum]

I just don't want to convert the sam to bam to trim alignments and then reconvert it to sam.

which tools are you referring to ?

by the way. There is no way to edit a BAM in place. You always have to write a new file (BAM or SAM).