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Hi @chapmanb .
In the past we typically ran analysis with bcbio from the input level of FASTQ or BAM files. We are happy with the results how scalable and reliable bcbio is.
To get a populatio…
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Hi,
I'm running the germline variant pipeline through CWL and cromwell, but it seems the CWL invocations of the bcbio codebase don't detect the GATK version correctly, causing the pipeline to stall…
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Hi,
I am trying to use PureCN with a vcf generated by Mutect2, but I get an error as follows when I run filterVcfMuTect2(vcf):
`Error in if (fractionContaminated > 0) { : missing value where TRUE…
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GATK4 VariantFiltration
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.3/org_broadinstitute_hellbender_tools_walkers_filters_VariantFiltration.php
I have no other ideas w…
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Hello, bcbio developers and users!
Thanks for the great pipeline!
I've read in the history that it is now possible to use vcfanno in RNA-seq analysis.
When trying this:
```
details:
- algori…
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For a PrintReads command that requires accessing the index, e.g. when specifying `-L` intervals, running locally works but running on `gs://` CRAM fails even if index is explicitly specified.
## Lo…
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Hi, Markus and PureCN devs! Could use some help getting around a new bug.
So I'm trying to run PureCN for a tumor sample without a matched normal. My VCF comes from Mutect2 and I am using a proc…
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This request was created from a contribution made by ABours on May 29, 2020 18:23 UTC.
Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360067695771-GenotypeGvcfs-has-formatting-issues-…
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https://github.com/galaxyproject/tools-devteam/issues/546
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A user reported seeing this error with SplitNCigarReads v4.8.1.0 -- "contig must be non-null and not equal to *, and start must be >= 1".
There was a similar issue ticket for the same exception a cou…