[DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

[Miguel Vazquez]

> 4. It looks like the *_pindel_input_* steps run for only 22-23 seconds
> which could indicate a problem with either the headers or the absence of
> the BAS file from the expected location.
>
>
I think that you just revealed the problem. There is in fact no BAS files
only BAM and BAI. There where BAS files for the test data HCC1143 which is
the one that in fact work. It seems like BAS files are not gathered by
gnos, could that be? or that my script fails to copy them. I'll try to
gather a different sample with my client and check.

Not knowing a thing about these files explains why I didn't notice. I'll
get back to you when I know more.

Best

Miguel
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