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Hello, i'm trying to run GATK4 BaseRecalibratorSpark in local in a nextflow pipeline, but I got every time the same error with this command :
**gatk-launch BaseRecalibratorSpark --spark-runner LO…
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Hello,
While using the GATK4 GenomicsDBImport (version >= 4.0.6.0) I'm keep getting the following error:
```
12:27:40.054 INFO ProgressMeter - Current Locus Elapsed Minutes Batches…
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Passing a .ped file to the VariantAnnotator tool does not work:
> gatk4 VariantAnnotator **-ped** my.ped --annotation PossibleDeNovo --variant my.vcf --output out.vcf
Result: A USER ERROR has…
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Hi there,
My question is if I should perform VQSR after running GLNexus and what is the recommended tool for doing this from a GLNexus output. Should I run Sentieon or GATK4 VQSR?
Thank you!
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If I run this command
hap.py-build/bin/hap.py Platinum_genome/split/chr1.recode.vcf 11_Haplotypecaller_indelrealigner/SRR622457_chr1.vcf -f 11_gatk_targetrealign/Chr1_SRR622457.bed -r /root/Work/ref-…
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Hi,
I wonder why "Allele_Frequency" filed is empty i.e "-" in *.mupexi output.
I am using vcf from GATK4-Mutect2.
Regards,
Raj
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_From @akiezun on April 21, 2015 22:48_
requirement for this ticket is to replicate the current gatk4 functionality (and make tests pass). We'll work from text-based recalibration tables for now.
_C…
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## Discussion \#1
```
bshifaw [3:59 PM]
Hi Chris,
The featured joint calling method is using NIO.
https://portal.firecloud.org/#methods/gatk/joint-discovery-gatk4/9/wdl
Is this the method you a…
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### Description of the bug
In `GATK4_POSTPROCESSGERMLINECNVCALLS`, the memory is handled in megabytes, but assigned to the java process in gigabytes.
See: https://github.com/nf-core/raredisease/bl…
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### Instructions
The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc. should…