SAMTools region switch

[ashkot]

Happy New Year to all.

I had a question regarding SAMTools region switch where we can specify chromosome number and region....I wanted to know if its possible to specify multiple regions in a text file.

I have several regions of interest so intead of running a command for each region, is it possible to have all the regions defined in a text file (sort of like a batch) and then simply specify that file in a single command?

Thanks in advance for your inputs.

Ashwin

[iansealy]

What samtools command are you using? "samtools view" can take a list of regions on the command line. "samtools mpileup" has the -l option for specifying a file containing a list of regions.

Cheers,
Ian

[ashkot]

Hi there,
I am using the view command and I want to convert a .bam file to .sam file, however i just want to analyze certain regions of the human genome, is this possible?

[iansealy]

Like I said, the view command can take a list of regions on the command line.

Cheers,
Ian