Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bam file increases in size following base recalibration

    I am doing some whole genomes and after the alignments, I am doing the indel-realign and base reaclibration steps. I am seeing an odd result. The bam file after the base recalibration increases in size as below:

    After the indel re-align, which is the same size as the originally mapped file:
    114G Aug 23 08:51 Nrml_IndelRealin.bam
    96G Aug 23 21:59 umr_IndelRealin.bam

    After base quality recalibration:
    126G Aug 25 20:40 Nrml_IndelRealin.BQSR.bam
    127G Aug 25 15:44 Tumr_IndelRealin.BQSR.bam

    Is this normal? Should the file size increase?

    Thanks

  • #2
    I haven't used it in forever but it may be keeping the old quality scores as well as the recalibrated ones. If that is default now there is an option to have it not do that (at least there was over a year ago when I last looked at this).

    Comment


    • #3
      Perhaps this is applicable in your case as well: http://gatkforums.broadinstitute.org...-recalibration

      Comment


      • #4
        I guess the size increase because the output qualities are less homogenous, ie the number of different letters coded as qualities increased and hence it's "harder" to compress.
        I guess such sequence is easier to compress:
        ",:,:,F,::F,,FFFF,,F,,,F:F::,F,F,F,F,F,FFF:,FF,F,:,:FF,F,F:FFFFFFFFF,FFFF:FFFFFF:FFFFFFFFFFFFFFFFFF,FF"
        than
        "/>-=-H'@>;/-BGCF-/B0.-F>B@@.J-B0C-F/B0CFF?'GC-F/70>FF/B0C=FHBHCFFHB0CGFH7GDGGHC@CFFHBGCFFHBGCFFGDI0GE" like in my case after recalibration.

        Comment


        • #5
          merge bam

          I am trying to create a combined bam file, from 8 files, to view on IGV

          I get this error

          What I can do ?

          base) javier@iMac-de-JAVIER BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.bam V350019555_L03_B5GHUMqcnrRAABA-551.bam V350019555_L03_B5GHUMqcnrRAAB(base) javier@iMac-de-JAVIER BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.bam V350019555_L03_B5GHUMqcnrR(base) javier@iMac-de-JAVIER BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.(base) javier@iMac-de-JAVIER BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.bam V350019555_L03_B5GHUMqcnrRAABA-551.bam V350019555_L03_B5GHUMqcnrRAABA-552.bam V350019555_L03_B5GHUMqcnrRAABA-553.bam V350019555_L03_B5GHUMqcnrRAABA-554.bam V350019555_L03_B5GHUMqcnrRAABA-555.bam V350019555_L03_B5GHUMqcnrRAABA-556.bam




          samtools: invalid option -- o

          the version es 1.3.1

          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
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          51 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X