Hi,
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?
For example, when invoking a command like:
samtools fixmate [*-rpc*] [*-O* *format*]
*in.nameSrt.bam out.bam*
...is out.bam guaranteed to still be name-sorted?
Same for rmdup etc.
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.
Thanks,
Anton
--
Version used:
samtools 1.3.1
Using htslib 1.3.1
Copyright (C) 2016 Genome Research Ltd.
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