Thanks all, the problem is solved. it appears that the warning message is not related to the bam header and the header is there already.

Hi everyone, I hope you are all great, I'm trying to convert my sam files into bam using the below command

samtools view -h -b -o file.bam file.sam

it worked fine but the output file has no header. I also tried to add the header using the two steps below

samtools view -H file.bam > header.sam  # extract header only
samtools reheader header.sam file.unique.bam

but the file still has no header. ps: when I run samtools view -h file.bam the output has a header, however, I'm getting an error message with each command that requires the header to be in the bam file. (for example, running bedintersect:

bedtools intersect   -s -header -a file.bam  -b file.bed > file2.bam 

I got the error message below

WARNING: -header option is not valid for BAM input)

any advice, please? your help is much appreciated. Surar