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Hi!
I spotted an error message in the flowing by text output while running a paired tumor-normal analysis:
Use of uninitialized value $sample in concatenation (.) or string at /usr/local/bin/var2vc…
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Hi,
the old webseite was specifying a non-profit license (Non-Profit Open Software License 3.0). I can not find any license statement on the Github pages. I formerly several times tried to seek con…
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I updated bcbio to use the more robust dbNSFP VEP annotation and am getting an error I haven't seen before.
[2017-02-06T18:02Z] Ensemble consensus calls for Kindred_87: samtools,platypus,gatk-hap…
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This is an approach that has been used in a few recent papers, and I think would be a worthwhile addition to the pipeline. There are some points to make:
- [ ] Ensure there are n > 1 methods available…
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Hi-
I can't seem to get snp_filter.py to work. This is the error I get:
$ snp_filter.py -n var.flt.vcf sampleDirectories.txt reference.fa
Traceback (most recent call last):
File "/Users/gotero/l…
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Hi,
Is there any way to increase sensitivity for somatic calling? For example, as I understand varscan imposes by default a 20% VAF limit for variants. Would be nice if this setting for varscan a…
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HI,
I wanna use VarScan to produce calls at variant sites and confident reference sites, but I can not find any parameters .
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Hi Chapmanb,
I try to go thought cancer somatic mutation pipeline, with tumor only mode. yaml config as follows:
Which is sample yaml file after delete normal part.
# https://www.synapse.org/…
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`git clone https://github.com/jeremiahsavage/cwl_valuefrom_literal.git`
with cwltool, a literal string specifed using `valueFrom` is passed to a subworkflow, and then to a tool, generating a 19 byt…
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I wanted to separate LOF and somatic HC and germline using processSomatic, but it requires a tabular input whereas I had generated VCF files. I want those VCF files and I want VCF files with LOF sepa…