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SAM to BAM --- samtools fail to read error

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  • #16
    Originally posted by dpryan View Post
    Ah, then since this is just hg18, you have a two options:

    1) Do what I suggested above, substituting the length of the various chromosomes in hg18 for the made up values I originally suggested. You would have to look up these values.

    2) Download the hg18 fasta file and run "samtools faidx" on it. You can then use the "-t" option that you tried before with the resulting .fai file. This is effectively the same as option 1, but requires less googling.

    BTW, I hope you replaced all of the coordinate information rather than just the chromosome (position 3). Otherwise whatever you do downstream will be messed up.
    Thank you!
    I did something similar and it is able to produce bam files now.

    Although kind of disappointed that i cannot use the tview option

    /usr/local/samtools-0.1.18/samtools tview test.bam
    [bam_index_load] fail to load BAM index.
    $ /usr/local/samtools-0.1.18/samtools index test.bam
    [bam_index_core] the alignment is not sorted (all-hg18_9815): 2498970
    > 2498636 in 1-th chr
    [bam_index_build2] fail to index the BAM file.


    • #17
      About the tview, from the way you run the command, I think u missed something. Have you sort the bam file using samtool sort command? If not, you have to sort them 1st, before doing indexing.

      samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>

      samtools index <sorted.bam>

      And from the tview run, u forgot to include the reference sequence

      samtools tview  <aln.sorted.bam> [ref.fasta]

      You can check out this post. This might help you
      Last edited by masterpiece; 09-27-2012, 07:38 PM.