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  • samtools view error after reheader

    I am currently having an issue with samtools view for conversion of .sam to .bam. After replacing the header of my .sam in order to match the ref contigs I think attempted the conversion and received the following output:

    $ samtools view -bS 1112-1.reheader.sam > 1112-1.reheader.bam

    [sam_read1] reference 'chr1' is recognized as '*'.
    [sam_read1] reference 'chr1' is recognized as '*'.
    [sam_read1] reference 'chr1' is recognized as '*'.
    etc.

    Basically for an endless number of lines.

    Has anyone seen a similar error?

  • #2
    Maybe this can help: http://seqanswers.com/forums/showthread.php?t=4719

    Comment


    • #3
      Hi - I received the same error. I also reheadered my sam file and then tried to convert to a bam and received the [sam_read1] reference 'chrX' is recognized as '*'.

      Did you ever figure out a solution to the problem?

      I noticed that samtools did write a bam file. So, I visualized it (after sorting and indexing it) and it appears that the rest of the chromosomes did convert except for the chrX. I have no reads there. Not surprising.

      Comment


      • #4
        I figured out the solution to my problem. Turns out that my sam file header had to be in the right format:

        The first line needs to be header.
        The second line needs to be a dummy read group line
        The next lines need to contain the chromosomes and their lengths.

        An example of a good header is as follows:

        @HD VN:1.0 SO:unsorted
        @RG ID:unknownReadGroup SM:unknownSample
        @SQ SN:chrI AS:ce6_32r_index LN:15072421
        @SQ SN:chrII AS:ce6_32r_index LN:15279323
        @SQ SN:chrIII AS:ce6_32r_index LN:13783681
        @SQ SN:chrIV AS:ce6_32r_index LN:17493785
        @SQ SN:chrM AS:ce6_32r_index LN:13794
        @SQ SN:chrV AS:ce6_32r_index LN:20919568
        @SQ SN:chrX AS:ce6_32r_index LN:17718854

        Once I deleted all the @SQ , @PG, @HD lines from my sam file and appended the above header text file to my sam file and tried to convert it to a bam - it worked beautifully.

        Comment

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