gatk

gatk copied to clipboard

Docker Container 4.4.0.0 - BaseRecalibrator ApplyBQSR - python not in env

5

Dear *, I just tested the Docker Container 4.4.0.0 (upgrade from 4.3.0.0) and my pipeline tried to execute BaseRecalibrator and ApplyBQSR. It crashed with a message: `/usr/bin/env: 'python': No such...

DanielAmsel

FastaAlternateReferenceMaker outputs empty fasta files for select genes from select VCF files

9

I am attempting to create fasta files from specific regions in approximately 270 VCF files. For every other region/gene I've looked at, I have not had this issue. For one...

lukaskon

Hi, I am on GATK v4.3.0.0 (CentOS) and would like to implement GermlineCNVCaller in my work. In an attempt to set up the conda environment (gcnvkernel) from zip using the...

snakesch

########code: docker run -it -v /media/sj/14t1:/data2 broadinstitute/gatk:latest java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.4.0.0-local.jar CNNVariantWriteTensors --output-tensor-dir /data2/example/results --reference /data2/example/1/hg19.fa --truth-bed /data2/example/hg19.hybrid.bed --truth-vcf /data2/example/hg19.hybrid.vcf.gz --variant /data2/example/NA12877.vcf.gz ##########result: 02:02:31.316 INFO NativeLibraryLoader -...

sujianed

Bundled jdk path was set to `scriptpath + "/gatkbundle/jdk/bin/java"` arbitrarily. It may be changed depending on the consensus of how to bundle a jdk with gatk.

gokalpcelik

Install the python-is-python3 package in our docker build

3

This symlinks /usr/bin/python to /usr/bin/python3, which can help avoid issues with scripts that reference the python binary directly. Resolves #8402

droazen

Funcotator - logic error for large deletions overlapping 5'UTR

6

## Bug Report ### Affected tool(s) or class(es) _Funcotator_ ### Affected version(s) - [x] Latest public release version [version v4.1.4.1] - [ ] Latest master branch as of [date of...

shenkers

Hi, I need to include the SnpCluster filter in VariantFiltration but the filtration is not working for me. I have included the other filters but I'm not sure about the...

Avinash-git-py

We should install the `python-is-python3` package during our docker build to create a symlink from `/usr/bin/python` to `/usr/bin/python3`. This would help avoid problems such as https://github.com/broadinstitute/gatk/issues/8402

droazen

The recent branch #8489 has demonstrated that there are some problematic edge cases in the pileup allele merging code that could cause pathological numbers of haplotypes to be handed to...

jamesemery