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Hi,
I am running tumor-normal somatic mutation pipeline and added svcall: cnvkit but found the following error.
[2015-11-21T23:55Z] *.edu: Timing: structural variation initial
[2015-11-21T23:55Z] *.e…
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Hello Gemini Team,
I am running into a strange problem when loading vcfs into gemini. The vcf that I have is generated using the bcbio ensemble tool and is based off of vcfs from freebayes, platypu…
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Hello,
I am running the tumor-only pipeline with ensemble calling using 4 variant callers (freebayes, gatk-haplotype, varscan, vardict). I have set numpass=1.
I have noticed that in the final vcfs t…
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I have run bcbio on whole-genome and realized that the GATK PrintReads step is a major bottleneck. Right now I run only whole-genome on one individual. I can see that "nct" option is not defined looki…
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I was trying to install libtorrent-rasterbar. I've successfully installed it before, not sure why it doesn't work now.
The exact copy-paste from command to error on Terminal:
```
$ brew install l…
ghost updated
6 years ago
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hello,
i just install PCGR and tried it with a vcf file i had laying around and this error was generated:
```
2017-11-28 22:09:37 [INFO] Number of block substitutions: 0
2017-11-28 22:09:37 [I…
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Terminates with error when installing spades.
See for output
https://gist.github.com/anonymous/91922c21dc68f1beffa6f34f15c620c0
Thanks.
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Error and change logs:
1.
Traceback (most recent call last):
File "/home/huangwt/Codes/somaticseq/modify_VJSD.py", line 116, in
with genome.open_textfile(right_files[0]) as vcf:
File "…
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docker run -v `pwd`:/data biocontainers/vcftools:latest vcf-merge data/muse.normalized.vcf data/somaticsniper.normalized.vcf data/varscan.snp.normalized.vcf data/radia.normalized.vcf
Unable to find i…
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Sorry, I am curious to know which parameter must be set in the project.yam in order to run phylowgs and bubble tree?
thanks!