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I ran SigProfilerAssignment for 396 HCC samples across a mutational matrix constructed using SigProfilerMatrixGenerator from PCAWG vcfs (lifted over to GRCh38) or vcfs from our own in house mutation …
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Hi I am trying to run SigProfilerExtractor in 225 tumor samples using GRCh38, which causes this error to occur:
```
Traceback (most recent call last):
File "/home/VCF_file/pyscript_vcf.py", line …
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For some runs it is desirable to annotate variant results from the pipeline with those that were also called in another pipeline. For example these could be variants from a CLIA/CAP pipeline and chec…
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Hello Markus,
How create normal panel from PureCN ?? In the description need only the AD but mutect2 and CreateSomaticPanelOfNormals has other format:
chr16 61946583 . AAT TAT,A . . BETA=1.00,1.…
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Hi all,
I'm getting an error with intervaltree while uploading the research SV VCF.
My pipeline is essentially to merge together multiple small cohorts of manta SV calls into one larger cohort usi…
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```
de decision tree crasht op het voorbeeld open exome sample van Marloes:
Command output:
classifying variants with decision tree ...
For input string: "0.475653&3.69905e-05&0.00182542&0.00…
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Following the README instructions for GRIPSS 2.3.5 for "germline mode" after having first created a somatic GRIPSS vcf in the same GRIPSS output directory:
`-sample SAMPLE_N \
-reference SAMPLE_T \
…
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Hi @ChristofferFlensburg,
We are facing some errors in SuperFreq trying to infer CNAs on RNA data.
The first error was related to the issue #100 (R 4.3.1 and SuperFreq 1.4.4):
> [E::bcf_hdr_p…
gbss2 updated
11 months ago
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Hi Christoffer,
When running superFreq, after about 12 minutes I get the following message:
```
Quitting from lines 331-366 (/tmp/Rtmp4d58zG/annette_report.Rmd)
Error in if (!hasNormal) return(NA…
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I was last successfully using PURPLE 3.8 and just tried 3.8.2, but PURPLE now is failing with "ERROR ... has invalid sample names"
14:23:49.303 [ERROR] vcf(DIR_PATH/SAGE-3.2/germline_genomewide/PAVE-…