after samtools sort -n, the bam header still has @HD SO:unsorted instead of @HD SO:queryname. Is this a bug?
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telos,
The author addresses that question in this this thread, specifically in point number 1 under "known issues". -
Thanks for pointing that out, I'd missed that. But to be clear, the issue I'm raising is not point number 1 ("Samtools does not write header "SO" tag"), but rather that Samtools doesn't change an existing "SO" tag after sorting, which results in an incorrect value for the the tag. I hope the author finds the time to correct this.Comment
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I believe the author was referring to both writing AND updating the SO tag with his statement.Comment
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