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Hi Brad,
I am here again for your help !! Sorry for troubling you again and again !!
I am getting below error now which seems like happening at the step of combining sample regions from strelka.…
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Im getting a error I haven't come across before.
Any Ideas?
sudo python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local --genomes GRCh37 --aligners bwa
Checking required depe…
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Hi Brad,
I found one sample in my batch stuck during the freebayes variant calling in the cancer somatic variant calling pipeline. I deleted this sample in the yaml file, the remaining pairs all fini…
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We are recently trying to update to Strelka2 for the first time. We are getting what seems to be plausible indel results but for SNVs, all SNVs fail filtering steps (almost all say "LowEVS", "IRC", o…
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Hi there,
I'm trying `speedseq somatic` analysis on my tumor/normal paired subset. I was wondering if I'm missing any parameter or argument because I've observed a extremely slow speed in the analysi…
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I try to use the tumor pai analisys. I have this error:
```
.
├── bcbio_sample.yaml
├── bcbiotx
├── BED
├── checkpoints_parallel
├── configuration
│ └── tumor.test.yaml
├── final
├──…
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Hi,
While parsing a freebayes VCF file, I noticed that the last two fields on tumour/normal depth counts etc seemed to be the wrong way round, for some of the calls. I am sure that this is an error…
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[mpileup] 2 samples in 2 input files
Set max per-file depth to 4000
ERROR: Cannot finish /usr/local/bin/run_varscan because failed to find /data/tmp/varscan.5536/mpileup
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The example configuration shows that you can use `germline` even with a `tumor` sample, but at least when re-running an already done analysis, this does not seem to happen.
Is there anything needed…
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VCF files produced by VARSCAN (v 2.4.2) separate multiple alleles in the Alt field with slashes instead of commas. It would be nice if the bcftools norm command could fix this.