Sambamba markdup usage help
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12 weeks ago

Hi!

I need so help regarding the usage of sambamba markdup. I have read the documentation but I don't quite understand.

  1. What is meant by insert size here?

     --hash-table-size=HASH_TABLE_SIZE
                        size of hash table for finding read pairs (default is 262144 reads);
                        will be rounded down to the nearest power of two;
                        should be > (average coverage) * (insert size) for good performance
    
  2. To get 100 GB here, should I just write: --sort-buffer-size 102400 ? The reason I wonder is that in sambamba sort you should specify e.g. Mb or Gb after the integer.

      --sort-buffer-size=SORT_BUFFER_SIZE
                            total amount of memory (in *megabytes*) used for sorting purposes;
                            the default is 2048, increasing it will reduce the number of created
                            temporary files and the time spent in the main thread
    

thx / Jonas

markdup sambamba • 118 views
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