On 7 Sep 2015, at 13:49, Tom Adlerteg <[email protected]> wrote:
> We are currently working on a tool for statistical analysis of substitutions
> and indels. As we see it is no longer supported to be able to print mapping
> qualities as a separate column when using samtools mpileup. This
> functionality would be most helpful to us, thus we wonder if there is a
> possibility that it will be reimplemented in future versions of samtools
> mpileup?
It seems like you're referring to mpileup -s, which still very much exists and
is supported.
John
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