Samtools view

[michalkovac]

Hi,

Is there a negative selection (like grep -v) option in samtools view command? I'd like to select reads coming from all chromosomes except one.

Thanks.
M.

[thurisaz]

What about piping samtools view to grep -v, so:

samtools view my_bam_file | grep -v Chr1

If you want to keep it, you could redirect the output of that to a file.

[michalkovac]

What about piping samtools view to grep -v, so:

samtools view my_bam_file | grep -v Chr1

If you want to keep it, you could redirect the output of that to a file.

I thought about it, but this will convert bam into sam leading to a loss of all tags and a header and running time will be considerably longer.