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  • bgold04
    started a topic Stand alone torrent variant caller -g request

    Stand alone torrent variant caller -g request

    Hi!

    I am trying to run the stand alone torrent variant caller on an 18-month old BAM file that was aligned to some version of hg19

    I am at the point where the caller is objecting to the fact that there appear to be two different runs in the file (I think).

    Here is the error message:

    ERROR: Multiple Samples found in BAM file/s provided. Torrent Variant Caller currently supports variant calling on only one sample.
    ERROR: Please select sample name to process using -g parameter.

    I have absolutely no clue where to put the -g parameter as requested.

    I looked at the BAM files using the header commands in Bamtools and find that there appear to be two runs, one named: ID:Y2PAB and another called ID:ZKWV4

    Each looks like it was aligned against a slightly different (possibly) hg19. The first: LB:hg19 and the second: LB:hg19_ucsc

    When I try to figure out how to put in the -g using help on the python command, or just trying -g, I get:

    variant_caller_pipeline.py -g
    Usage: variant_caller_pipeline.py [options]

    variant_caller_pipeline.py: error: no such option: -g

    ergo, this appears to be a difficult problem…

    Suggestions? Work-arounds?

    I have found the Ion Torrent Sample Manager in GitHub that is giving rise to the error message, but
    I still have no solution to how to use -g

    Last edited by bgold04; 01-10-2015, 04:25 PM. Reason: tiny update

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