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How to export gistic markers? #622
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Hi @BioComSoftware , Not an author of CNVkit, but reading the code I see "gistic" export is only partially implemented Adding the following chunk of code right after L1882 of your own
Hope this helps. |
Thanks for the fast help! |
I added the above code to my copy of cnvkit, and it appears to be creating a properly formatted markers file. I will continue testing. |
Did the file generated by this function work properly with Gistic? |
Hi @BioComSoftware, did you have a chance to test if the file is correct, so that we could merge the associated PR #623? |
Hi Kirill,
I did get a chance to test it - but I'm not sure the results will be
helpful.
The export did run through to completion without error, and did produce
(what looks like) a properly formatted markers file.
However, when I attempted to use the markers file with GISTIC (in
conjunction with the SEG file created by CNVKIT) - GISTIC failed to run
and ended with errors. I was not able to confirm the errors were
specifically caused by the markers file, since I managed to get GISTIC
to run without a markers file at all, and stopped pursuing it.
Best,
Mike
Kirill Tsukanov wrote on 6/23/2021 7:13 PM:
…
Hi @BioComSoftware <https://github.com/BioComSoftware>, did you have a
chance to test if the file is correct, so that we could merge the
associated PR #623 <#623>?
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Hi @BioComSoftware , Thanks for your feedback! As discussed here, for now there could be a small inconsistency between Thanks in advance Mike. |
Within
export.py
there's aexport_gistic_markers(cnr_fnames)
.Also within
export.py
, there's a dictionary...I've tried exporting a gistic marker file using
cnvkit.py export gistic
but I get an error...What is the usage to get a gistic marker output file from cnvkit?
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