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  • removing chromosomes from a bam file.

    I'm trying to upload a bam file, from an alignment to GRCh38 that I've done, to a google genomics dataset, associating it with the reference set for GRCh38. The reason it fails given in the logfile reads:

    Code:
    reference names must be a subset of those of the requested
        reference set: missing ["chr1" "chr10" "chr11" "chr11_KI270721v1_random" "chr12"
        "chr13" "chr14" "chr14_GL000009v2_random" "chr14_GL000194v1_random" "chr14_GL000225v1_random" ...
    It goes on to list another 40 or so fragments. If I do a quick

    Code:
    samtools idxstats cal1.bam
    I do indeed get a whole bunch of chromosome fragments listed. The best I can come up with is that the referenceset on google genomics doesn't like all the fragments, thus the reference names must be a subset message.
    The obvious workaround to test this, is to remove those chromosomes from the bam file. Unfortunately,

    Code:
    samtools view -b cal1.bam chr1 chr2 chr3 > cal-sub-1.bam
    samtools index cal-sub-1.bam cal-sub-1.bai
    samtools idxstats cal-sub-1.bam
    returns a bam file that indeed, removes all the reads from the fragments from the bam file. It still lists the actual fragments though, which in turn, when I try and load to the google genomics dataset, gives me the same error.

    How to I remove all references to the fragments from the bam file? Or is that not what the googlegenomics upload is objecting to.

    Thanks
    Ben.

  • #2
    Did you check the headers from the subset BAM files? Those may still contain the offending chromosomes.

    Comment

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