Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Samtools sort vs Picard Sortsam

    Hi all,

    Which is a better pick for sorting large SAM files in terms of memory requirement and run time: sortSam from Picard or Samtools sort function. Could you please direct me to the thread if it is already discussed and i missed it.

    Thank you,

    Rahul

  • #2
    I want to know SortSam vs samtools sort, too.

    I think MarkDuplicates is better than rmdup because the former can handle duplicates across break points.

    Comment


    • #3
      Why don't you just try?

      Comment


      • #4
        Originally posted by sklages View Post
        Why don't you just try?
        Because they give the same results after I try. I think there might be differences in edge cases, for example, when it is piped from bwa-mem. But I don't know what the edge cases are.

        Comment


        • #5
          So if you get the same results in terms of mem and runtime for huge files, just decide for the one you're more familiar with. Edge cases are usually very specific, so if you don't encounter any problems with your regular files, no need to worry :-)

          Comment


          • #6
            I think Picard's sortSam puts a line in the header indicating that the file is sorted, which samtools does not. But for lots of applications this doesn't matter.

            Comment


            • #7
              Originally posted by swbarnes2 View Post
              I think Picard's sortSam puts a line in the header indicating that the file is sorted, which samtools does not. But for lots of applications this doesn't matter.
              Are you sure about that? The header is grabbed from the first tmp file written.

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Latest Developments in Precision Medicine
                by seqadmin



                Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

                Somatic Genomics
                “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
                05-24-2024, 01:16 PM
              • seqadmin
                Recent Advances in Sequencing Analysis Tools
                by seqadmin


                The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
                05-06-2024, 07:48 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 01:32 PM
              0 responses
              10 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 05-24-2024, 07:15 AM
              0 responses
              199 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 05-23-2024, 10:28 AM
              0 responses
              221 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 05-23-2024, 07:35 AM
              0 responses
              232 views
              0 likes
              Last Post seqadmin  
              Working...
              X