Stand alone torrent variant caller -g request

[bgold04]

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

https://github.com/iontorrent/TS/blob/master/Analysis/VariantCaller/SampleManager.cpp