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  • 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>[email protected]@.J-B0C-F/B0CFF?'GC-F/70>FF/[email protected]" 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) [email protected] 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) [email protected] BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.bam V350019555_L03_B5GHUMqcnrR(base) [email protected] BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.(base) [email protected] 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

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