The format for somatic variant file is unclear.
The README lists 3 columns:
1.:PMCFREQ Tumour variant frequency
2.<anotherSample>:PMCFREQ Normal variant frequency
3.CANONICAL: Value "YES" would indicate canonical transcript, only these will be included.
I'm imaginging a file full of the following:
0.99 0.50 yes
0.83 0.49 yes
Should these be SNV or indels? Where does the position and chromosome location go?
I'm having trouble with the NDE pipeline. When running nde_wrapper.py, should the ContraOut_List.txt file have the full paths to the contra out folders? I am feeding in the folders generated by contra.py, but get an error saying bad paths. I've tried it with and without paths and neither way works.
Example:
/users/PAS1208/osu0972/awebb/cynthia/Rubicon/contra_cnv/GBM30vsBaseline
where GBM30vsBaseline contains the table folder. I've tried it with and without a slash at the end.
nde_wrapper.py runs through, but generates files full of NA. I get the following as warnings:
Finished processing out to NDE_OUTDIR/renorm_list.txt
Bad paths:
059-01vsBaseline 059-03vsBaseline 059-04vsBaseline 059-06vsBaseline 059-08vsBaseline 059-09vsBaseline 059-11vsBaseline 059-12vsBaseline 059-14vsBaseline 059-19vsBaseline 059-24-PoolAvsBaseline 059-25vsBaseline 059-26-PoolBvsBaseline 059-27vsBaseline 059-29-PoolAvsBaseline 059-32vsBaseline 059-33-PoolBvsBaseline 059-34vsBaseline 059-37vsBaseline 059-38vsBaseline 059-40vsBaseline 059-41vsBaseline 059-42vsBaseline 059-43-PoolCvsBaseline 059-45-PoolCvsBaseline 059-46vsBaseline 059-47vsBaseline 059-48-PoolBvsBaseline 059-49vsBaseline 059-50vsBaseline 059-53vsBaseline 059-55vsBaseline 059-56-PoolCvsBaseline 059-57vsBaseline 059-58vsBaseline 059-59vsBaseline 12054-10-T1vsBaseline 12054-11-T1vsBaseline 12054-12-T1vsBaseline 12054-1-T1vsBaseline 12054-2-T1vsBaseline 12054-3-T1vsBaseline 12054-4-T1vsBaseline 12054-5-T1vsBaseline 12054-6-T1vsBaseline 12054-7-T1vsBaseline 12054-8-T1vsBaseline 12054-9-T1vsBaseline 131vsBaseline 57BvsBaseline 77M1T1vsBaseline 77T1vsBaseline GBM30vsBaseline
Finished processing out to NDE_OUTDIR/summary_ex.txt
Finished writing whole-gene data to NDE_OUTDIR/summary_wg.txt
Finished writing errors to NDE_OUTDIR/debug/2_getExons_errors.txt
Thanks for your help!
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I have 2 issues:
The format for somatic variant file is unclear.
The README lists 3 columns:
1.:PMCFREQ Tumour variant frequency
2.<anotherSample>:PMCFREQ Normal variant frequency
3.CANONICAL: Value "YES" would indicate canonical transcript, only these will be included.
I'm imaginging a file full of the following:
0.99 0.50 yes
0.83 0.49 yes
Should these be SNV or indels? Where does the position and chromosome location go?
I'm having trouble with the NDE pipeline. When running nde_wrapper.py, should the ContraOut_List.txt file have the full paths to the contra out folders? I am feeding in the folders generated by contra.py, but get an error saying bad paths. I've tried it with and without paths and neither way works.
Example:
/users/PAS1208/osu0972/awebb/cynthia/Rubicon/contra_cnv/GBM30vsBaseline
where GBM30vsBaseline contains the table folder. I've tried it with and without a slash at the end.
nde_wrapper.py runs through, but generates files full of NA. I get the following as warnings:
Finished processing out to NDE_OUTDIR/renorm_list.txt
Bad paths:
059-01vsBaseline 059-03vsBaseline 059-04vsBaseline 059-06vsBaseline 059-08vsBaseline 059-09vsBaseline 059-11vsBaseline 059-12vsBaseline 059-14vsBaseline 059-19vsBaseline 059-24-PoolAvsBaseline 059-25vsBaseline 059-26-PoolBvsBaseline 059-27vsBaseline 059-29-PoolAvsBaseline 059-32vsBaseline 059-33-PoolBvsBaseline 059-34vsBaseline 059-37vsBaseline 059-38vsBaseline 059-40vsBaseline 059-41vsBaseline 059-42vsBaseline 059-43-PoolCvsBaseline 059-45-PoolCvsBaseline 059-46vsBaseline 059-47vsBaseline 059-48-PoolBvsBaseline 059-49vsBaseline 059-50vsBaseline 059-53vsBaseline 059-55vsBaseline 059-56-PoolCvsBaseline 059-57vsBaseline 059-58vsBaseline 059-59vsBaseline 12054-10-T1vsBaseline 12054-11-T1vsBaseline 12054-12-T1vsBaseline 12054-1-T1vsBaseline 12054-2-T1vsBaseline 12054-3-T1vsBaseline 12054-4-T1vsBaseline 12054-5-T1vsBaseline 12054-6-T1vsBaseline 12054-7-T1vsBaseline 12054-8-T1vsBaseline 12054-9-T1vsBaseline 131vsBaseline 57BvsBaseline 77M1T1vsBaseline 77T1vsBaseline GBM30vsBaseline
Finished processing out to NDE_OUTDIR/summary_ex.txt
Finished writing whole-gene data to NDE_OUTDIR/summary_wg.txt
Finished writing errors to NDE_OUTDIR/debug/2_getExons_errors.txt
Thanks for your help!