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Run Strelka2 to find germline variants in paired tumor-normal samples.
python /Software/strelka-2.9.10/bin/configureStrelkaGermlineWorkflow.py \ …
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Hi,
I posted this issue on the Vardict GitHub page but got no reply, so apologies for duplicating it here.
I am trying to run Vardict on WES data from paired tumour and germline sample. I used BWA m…
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Hello,I want to ask whether the demo/runDemo.sh /pathogenicVariants.vcf file is lost? I can't find pathogenicVariants.vcf mentioned in runDemo.sh file.
Thnaks for your help.
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"""
**2. Single somatic MAF file**
• Includes all somatic mutations (point/indels) along with annotation, filtering, FACETS CCFs, neoantigen predictions (neo_* columns from somatic_variants/neoantig…
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Hi, I am running somatic variant calling with tumor-only samples. I am wondering how to get the number of reference vs. variant reads for each variant. I notice that some variants have a `MAP_VAF` val…
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Hello,
We have several samples that were created using "Trusight RapidCapture Cancer Panel" on which I ran the default configuration of bcbio for variant calling (see example of the config below). …
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Hi,
I was trying to run ```cpsr``` but it popped up an error when generating output file. Can you check for me please? Thank you in advance!
```
2019-05-06 17:15:26 - cpsr-writer - INFO - STEP…
jxshi updated
5 years ago
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Hi,
I am getting very high number of snvs from somatic mutation calling. Interestingly, when I compare strelka snv calls with the ICGC's snv calls (ICGC's consensus calls), some samples have ridicu…
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Hello,
I'm noticing some errors when running joint calling with multiple variant callers and ensemble mode. The input files are the same as here: https://github.com/bcbio/bcbio-nextgen/issues/2688#…
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Hi guys,
I have a strange error that has popped up inconsistently in the pipeline. It looks like it is crashing because of some non-ascii character that it is attempting to write.
The strange t…
waemm updated
5 years ago