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List of somatic callers at https://omictools.com/somatic-snp-detection-category
- [x] **MuTect2:** ready
- [x] Strelka: very cumbersome to use https://sites.google.com/site/strelkasomaticvariantcalle…
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I've seen similar issues to this, but they're closed. I did update to current development version just before rerunning this and i get the same error. I will say upfront that it is "possible" that t…
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Manta seems to run cleanly on some of my samples but not others that were all aligned and processed together with bcbio.
Config template:
details:
- analysis: variant2
metadata:
batch:
…
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Hi Brad,
I am using four vairant callers: mutect2, freebayes, vardict, varscan and ensemble: numpass: 2 criteria to run the turmor-germline cancer variant calling pipeline for 17 pairs in the new 1.0…
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Hi Bioconda developers,
I saw that the VarScan (version 2.4.2) is available in the recipes. I am wondering, however, what the policy is for adding previously released versions of a package.
My concr…
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I am trying to ease debugging by creating the cwl pattern used by the gdc pipeline using just unix tools, as this pattern runs in a fraction of the time while using the same cwl features.
`git clon…
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Thanks for the new project! This looks quite interesting. I wanted to give this a quick test and ran into the following problem. I have activated cloud dataflow API (and the others) and I thought t…
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I have centos 7 and I have this error
```
2017-05-26T16:09Z] INFO 16:09:01,462 ReadShardBalancer$1 - Loading BAM index data
[2017-05-26T16:09Z] INFO 16:09:01,486 ReadShardBalancer$1 - D…
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Hi Brad,
I am running tumor-germline somatic variant calling pipeline. The bcbio-nextgen is 1.0.0 development version and all the --data have been updated into the newest in November 3rd including db…
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Hi Brad, I have tried to update my bcbio with bcbio_nextgen.py upgrade -u development --tools --data and But I receive.
I guess the problem is with age-metas dependencies.
Thanks!
Unsatisfiab…