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I'm trying to install the latest stable version and it's failing, something to do with a badly formatted YAML file. Here's what I'm running:
```
bcbio_path=/export/home/ncit/external/a.mizeranschi…
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Hi,
During a bcbio RNAseq analysis the peak load per cpu shot up to 600 on multiple machines, where a load of 60 per CPU should be the max. Nothing else was running on these machines.
```
# Te…
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Hi,
I am testing the same sample (~400 MB bam file with just chromosome X) for RNA-seq variant calling using GATK3 and GATK4.
Here is my config files, both are exactly the same except for `tools…
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Hi,
We're looking into leaning a bit more on Peddy for QC of our trio analysis. However, I noticed bcbio does not take the defined trio's into account and uses a single sample vcf instead of the jo…
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I think we decided today to implement CollectHSMetrics from GATK4/Picard (they're the same tool nowadays).
https://github.com/mskcc/vaporware/issues/389
```
gatk CollectHsMetrics \
I=in…
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This would greatly reduce my need to modify WDL scripts to start where I have data already processed. For example, if a script goes BAM-->coverage-->CNVs, if I have already collected coverage on my BA…
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Tool: GATK4 ApplyBQSR (~GATK3 PrintReads)
Location: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_bqsr_ApplyBQSR.php
Version: [4…
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There was an error: "Input files reference and reads have incompatible contigs: Found contigs with the same name but different lengths:
contig reference = MT / 16569
contig reads = MT / 16571."
A…
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Re: #247 and other things not yet discussed at length.
Finalize post-processing and annotation of germline calls. Something like this:
![image](https://user-images.githubusercontent.com/4834443/58…
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Hello!
I am using the `gatk-variant` template and have encountered some issues I would really appreciate any help with.
Upon executing the following command:
`bcbio_nextgen.py /n/data1/hms/db…