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I'm having some issues with```surpyvor upset```. I'm trying to process .vcf from GATK4 germline CNV caller, but their format is a bit weird. I modified it a bit and added some information to this .vcf…
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## Feature request
### Tool(s) or class(es) involved
VariantFiltration
### Description
While running variantFiltration, I have encountered the following error:
```
java.lang.NumberFormatExce…
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Error type 1:
gatk --java-options "-Xmx32G -XX:ParallelGCThreads=8 -Djava.io.tmpdir=/tmp" SplitNCigarReads --spark-runner LOCAL -I 10_mkdup/SAMD00025146_mkdup.bam -R Gallus_gallus.GRCg6a.d…
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Hello,
I'm trying to use GATK4 (4.1.8.1) on an Ubuntu (16.04) machine. The machine is a "PowerLinux" machine and I'm guessing that the most relevant info for the following problem is that it is a p…
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Dear GATK team,
Is it possible to run haplotypecaller using FPGA cards on GATK4?
thank you
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### Actual Behavior
I install ensembl-vep from bioconda but the version is not the indicated 102.0, but 89.9
### Expected Behavior
the syntax has changed a lot from the old to the new…
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Installed latest verison of bcbio but running into errors even after activating the environment
bcbio_nextgen.py fc_dir ./sample_gmi.yaml -n 8
Running bcbio version: 1.2.3
global config: /pathto/…
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When set, the # argument leads to a message saying it is not recognized (idem with shorter notation -new-qual).
* is this parameter obsolete with this version of GATK4 (4.1.6.0) and should it be re…
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I am running BaseVarC in a docker container using nextflow, I am feeding it a BAM file from BWA MEM and calling each chromosome independently (using 1-n not 0-n).
However, BaseVarC ends with error …
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Hi,
When I used the `enable-all-annotations` option to run Mutect2, it failed.
```
~/software/gatktools/gatk-4.1.3.0/gatk Mutect2 \
-R ~/database/hg19/gatk_bundle/ucsc.hg19.fasta \
-I sample.re…
xiucz updated
4 years ago