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Hi @tianshilu,
You uesd GATK3 in the somatic.pl,but now when I use GATK3, the RealignerTargetCreator, IndelRealigner and PrintReads function of GATK3 can not be found in my GATK3,may be GATK4 replace…
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Once GATK4.5.0.0 is out on DockerHub, we'll want to update it here
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my code end ENV:
config file:
backend {
providers {
SLURM {
actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
config {
files…
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Using cromwell v36, not all log output appears to be captured even if log level set to DEBUG.
For example, using the HaplotypeCallerGvcf_GATK4 reference on GitHub, if an non-existent path is provid…
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### Description of the bug
Then GATK4_BEDTOINTERVALLIST sometimes fails when using a variety of references genomes due to the incorrect creation of the genome.dict or exome.bed file from the refere…
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Hi,
I got a timeout exception during cache copying on AWS S3. The cache file size is 133GB. Given the file size, more time should be allowed for cache copying. Is there any config option that can t…
XLuyu updated
4 years ago
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gatk_hc.sh script prints `Exception in GATK log ./Logs/GATK4_HC/$sample/$sample.log` to ./Logs/GATK4_HC_error_capture/$sample.err files, even if exception isn't present in .log file.
https://gith…
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> [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/bio…
mr-c updated
7 months ago
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[//]: # (Please do not include your AWS account or credentials as part of the bug request.)
**Describe the Bug**
[//]: # (Please describe the behavior that you are seeing with as many details …
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Hello,
I am writing to you by email about your reconCNV tool. First, I would like to thank you for developing it.
Unfortunately, to use it, I'm “hijacking” its way of functioning, so I don't kn…