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?
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?
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