Use SAM files in ref_map.pl

Question

[Hayler Edu]

Hello everyone, today I'm trying to use ref_map.pl, but I have a problem.

On the STACKS website, I can see that ref_map.pl recognizes .SAM files, but when I try to execute the software, I get an error that says it's looking for a .bam file.

Does anyone know if I need to use a specific command to indicate to ref_map.pl to open the SAM file?

[swbarnes2]

No one can help you with a random perl script that none of us can read. Post the code, or post to where you found the script.

Answer 1

[GenoMax]

I get an error that says it's looking for a .bam file.

If that is the case and you have SAM files then you need to convert them into BAM format using samtools.

The help page for the program says this in first para:

The ref_map.pl program expects data to have been aligned to a reference genome, and can accept data from any aligner that can produce BAM formated files.