Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Using Dindel: callback and output on realigned BAM

    Hello, when I'm using dindel, I want to output the realigned BAM file for the genome viewer. So I used the option --outputRealignedBAM, and then I had many many files. Is it possible that I merge all the realigned BAM files into one? How can I do that?
    Also, I used the callback script provided by the author:
    #!/bin/bash
    samtools view $1 >> $2.sam
    echo $3 $4 $5 >> $2.windows
    rm $1
    But it's not working. Any idea to improve this?

    Many thanks!

  • #2
    Any one has any idea?

    Comment


    • #3
      This is how I am running it right now. I have a file called processRealignedBams.sh, that contains the shell script you posted above.Then I am just running dindel (step 3) using the options

      Code:
      --outputRealignedBAM --processRealignedBAM processRealignedBams.sh
      Seems to work fine with me.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      66 views
      0 likes
      Last Post seqadmin  
      Working...
      X