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I am looking at using GATK and first checked at the docker image using **_docker pull broadinstitute/gatk_**
this container image has 1460 vulnerabilities and a lot of them are critical.
Then…
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### Description of the bug
Hi! I was expecting a mapped BAM index to be output alongside the final mapped BAM when running fastquorum in high-throughput mode. Perhaps I'm missing something from my pa…
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Once GATK4.5.0.0 is out on DockerHub, we'll want to update it here
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## Bug Report
### Affected tool(s) or class(es)
GenotypeGVCFs
### Affected version(s)
4.6.0.0
### Description
When I was doing GenotypeGVCFs from GenomicsDB of 420 samples, the process …
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**Is your feature request related to a problem? Please describe.**
`snappy` currently uses an old, non-free version of GATK.
**Describe the solution you'd like**
We should mode to GATK version 4,…
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Hi Misha,
For hard-calling SNPs using GATK, the function for GenomeAnalysisTK.jar / UnifiedGenotyper is no longer supported in the current version; instead it's replaced by HaplotypeCaller.
htt…
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Excerpt from PiscesBioinformaticsApplicationNote_SupplementaryMethods.docx:
"The highest quality results can be obtained by using an indel-realigned, stitched bam."
"The full Pisces Suite workfl…
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Either in Hello World or a generic Part 2 (before Hello GATK)
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The GATK SV clustering algorithm is here:
https://gatk.broadinstitute.org/hc/en-us/articles/4418051427867-SVCluster-BETA
Do we need their concordance code? Check with Alba.
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Hi, I am installing UVP-2.7.0 following the conda installation instruction.
However, only gatk3 and gatk3-register are found in the /bin directory in the uvp-2.7.0 conda env.
So error occur when gat…