message: update readme to reflect new tools
diff: @@ -167,10 +167,8 @@ samples. You can use freebayes to detect the variants, following these steps:
  * Ensure your alignments have **read groups** attached so their sample may be
  identified by freebayes. Aligners allow you to do this, but you can also use
  [bamaddrg](http://github.com/ekg/bamaddrg) to do so post-alignment.
  -* **Sort** the alignments (e.g. bamtools sort).
  -* **Mark duplicates**, for instance with [samtools
  -rmdup](http://samtools.sourceforge.net/) (if PCR was used in the preparation of
  -your sequencing library)
  +* **Sort** the alignments (e.g. [sambamba sort](https://github.com/biod/sambamba)).
  +* **Mark duplicates**, for instance with [sambamba markdup](https://github.com/biod/sambamba) (if PCR was used in the preparation of your sequencing library)
  * ***Run freebayes*** on all your alignment data simultaneously, generating a
  VCF. The default settings should work for most use cases, but if your samples
  are not diploid, set the `--ploidy` and adjust the `--min-alternate-fraction`
  