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Hello!
Starting this thread to update variant calling validation in bcbio.
Users reported some validation results,
based on NA12878 and another 6 NA12XXXXX samples,
showing that gatk4.1 + bc…
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Hi,
I have created normalDB with PureCN 1.14.3, and was trying to proceed with the GATK4 tumor only VCF.
```
Rscript \
/usr/local/lib/R/site-library/PureCN/extdata/PureCN.R \
--co…
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I'm running GATK4's SplitNCigarReads in the Broad best practice workflow for [RNAseq short variant calling](https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discover…
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https://github.com/common-workflow-lab/2020-covid-19-bh/blob/master/SOP-gatk-SARS-CoV-2.md
- [x] needs a GATK4 version, GATK3 is not Free nor Open Source so we can't use it
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Hello:
I got an error when running `PureCN.R` according to the **PureCN best practices**, as shown below.
Could you help me how to solve it?
```
# Without a matched normal (minimal test run)…
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The new release of GATK 4.1.0.0 comes, also, the mutect2 is out of beta version. I think we should integrate the mutect2 result with purecn more better now.
xiucz updated
4 years ago
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**Question:** Is there a way to create a template and run all the available QC tools on FASTQ files as a stand alone step (and for that matter BAMs)? Which can then be collated using multiQC.
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Hi ,
The parameter `--max-alternate-alleles` seems no longer in the new version gatk4.1.7.0...How can I get only one alt allele in the vcf, or how to filter it?
Thank you,
Xiucz
xiucz updated
4 years ago
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Hello IUC &
@davebx ,
Regarding the wrapper of [GATK4 Mutect2](https://github.com/galaxyproject/tools-iuc/blob/master/tools/gatk4/gatk4_Mutect2.xml), I would like to ask you about the reason of n…
lgpdv updated
4 years ago
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Hello,
We've been using GATK4 DepthOfCoverage. I noticed this:
log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage).
log4j:W…