[swbarnes2]

The samtools view expects a .bam file. test.sam.out is a sam file. You can just look at it with head or whatever to see if the read groups took.

Also, if that perl script isn't working, just try something else. Picard does so many useful things, you might as well get it if you don't have it already.

And converting the .bam to a .sam is a little silly. Can't you pipe the .bam through samtools view into the perl script?

[jwhite]

The samtools view expects a .bam file. test.sam.out is a sam file. You can just look at it with head or whatever to see if the read groups took.

Also, if that perl script isn't working, just try something else. Picard does so many useful things, you might as well get it if you don't have it already.

And converting the .bam to a .sam is a little silly. Can't you pipe the .bam through samtools view into the perl script?

Thanks for your help. I thought samtools view also viewed sam files--even though 'less' works too.

Yes, I can get Picard. I've avoided it because I did not want to deal with java for this pipeline.

Yes, I can pipe the view output into the perl script. Hadn't though about that.

But my main issue has been that samtools view has been throwing up these errors when I supply BAM files as imput. These BAM files were generated by samtools; that's what I don't get. Something has been altered in the BAM files such that they are no longer readable by samtools.

Joe