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For @ldgauthier, upon her return from the Montreal workshop. We would like to know if this is expected behavior from HaplotypeCaller.
Researcher has uploaded read-level data to our FTP site. I've r…
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Allow users to specify custom Docker images to be used to launch notebooks.
Soo Hee Lee from the DSP Comms team: "We need to be able to run the Docker image broadinstitute/gatk:4.0.5.0 and run a Spar…
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@SHuang-Broad commented on [Tue Sep 13 2016](https://github.com/broadinstitute/gatk-protected/issues/706)
[Here](https://github.com/broadinstitute/gsa-unstable/pull/1475), but the alt allele removal …
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I using following command to filter my vcf file:
```
gatk --java-options "-Xmx4g" FilterMutectCalls -O Filtered.vcf -V Try.vcf.gz
```
And failed with following info:
```
Using GATK jar /ro…
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## Bug Report
java.lang.OutOfMemoryError when 'java -jar /usr/hpc-bio/gatk/gatk-package-4.1.2.0-local.jar' sometimes, but there is a lot of memeory yet.
And then all features can not be used.
…
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I've traced the error to vt normalize in this line of ggd-run.sh:
```
bcftools view -f PASS $vcf_file | bcftools annotate -x "^$fields_to_keep" -Ov | vt decompose -s - | vt normalize -r $ref -n - …
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Hi!
when running variant calling on hg38 with disambiguate on mm10:
```
details:
- algorithm:
aligner: bwa
coverage: /path/coverage.bed
coverage_interval: regional
disambig…
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Hi,
I just noticed a new `gatk4` in the bioconda channel,
`gatk4 4.1.4.0 1 bioconda`
and I was curious to figure out what had changed. However, when I ch…
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Hi!
Thanks again for the fantastic tools you are making. Feel bad for coming only to complain about something, whereas in fact they are working great 99.9% of the time.
I'm now trying to run the…
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right now you get this which is bogus on many levels (duplicated and confusing categories, confusing tool names etc). We need to put more order into this. @vdauwera can you help come up with a better …