MarkDuplicatesSpark documentation tweak (#7191) (#7535)

Co-authored-by: Derek Caetano-Anollés <[email protected]>

src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSpark.java

@@ -41,7 +41,7 @@
  * Here are some differences of note between MarkDuplicatesSpark and Picard MarkDuplicates.
  *
  * <ul>
- *  <li>MarkDuplicatesSpark processing can replace both the MarkDuplicates and SortSam steps of the Best Practices <a href="https://software.broadinstitute.org/gatk/documentation/article?id=7899#2">single sample pipeline</a>. After flagging duplicate sets, the tool automatically coordinate-sorts the records. It is still necessary to subsequently run SetNmMdAndUqTags before running BQSR. </li>
+ *  <li>MarkDuplicatesSpark processing can replace both the MarkDuplicates and SortSam steps of the Best Practices <a href="https://software.broadinstitute.org/gatk/documentation/article?id=7899#2">single sample pipeline</a>. After flagging duplicate sets, the tool automatically coordinate-sorts the records. It is recommended to subsequently run SetNmMdAndUqTags before running BQSR. </li>
  *  <li>The tool is optimized to run on queryname-grouped alignments (that is, all reads with the same queryname are together in the input file). If provided coordinate-sorted alignments, the tool will spend additional time first queryname sorting the reads internally. This can result in the tool being up to 2x slower processing under some circumstances.</li>
  *  <li>Due to MarkDuplicatesSpark queryname-sorting coordinate-sorted inputs internally at the start, the tool produces identical results regardless of the input sort-order. That is, it will flag duplicates sets that include secondary, and supplementary and unmapped mate records no matter the sort-order of the input. This differs from how Picard MarkDuplicates behaves given the differently sorted inputs. </li>
  *  <li>Collecting duplicate metrics slows down performance and thus the metrics collection is optional and must be specified for the Spark version of the tool with '-M'. It is possible to collect the metrics with the standalone Picard tool <a href='https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_sam_markduplicates_EstimateLibraryComplexity.php'>EstimateLibraryComplexity</a>.</li>