Re: [Samtools-help] some samtools commands require sorted input - is the output guaranteed to be still in the same sort order?

[James B. <jk...@sa...>]

On Fri, Mar 17, 2017 at 12:07:47PM +0900, Anton Kratz wrote:
> many samtools commands expect the input to be either name-sorted or
> coordinate-sorted, respectively.
> 
> Is it guaranteed that the output of these commands is still in the same
> sort-order as the input?

I cannot think of any commands which change the sort order other than
the obvious ones (samtools sort, collate).

> I am doing a process along the lines of fixmate --> rmdup --> index -->
> flagstat and I am wondering if I have to sort again before each
> intermediate step.

You will need some sort steps as not all of these processes take the
same order.  The manpage for fixmate claims to need name sorted data,
but I *think* name collated is sufficient and samtools collate would
do as a faster alternative.  I say "think" because the man page
definitely implies this isn't true, but maybe it's just a historical
quirk.  Other parts of your pipeline require position sorted data, eg
samtools index.  If you're starting from aligner output then there is
high probability it's already in name collated order anyway. (It may
vary by aligner though, so check.)

Note it's worth remembering within a unix pipe that using uncompressed
BAM is typcially the fastest interchange, as you'll typically only
want to do compression at the final stage.

James

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