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Hi folks. @chandrans and I have laid out some plans towards updating GATK4 docs for the January 9 release. Our approach is to prioritize documentation around stable Best Practice Workflows. On the doc…
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We've started seeing an authentication error in our project after we upgraded to 0.23.1, the issue also seems to be present in 0.24.0. Reverting to 0.22.0 solves the issue.
We start seeing the f…
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Hi @chapmanb .
There was a nice GA4GH BAM/VCF compression workshop yesterday. See here for the slides.
https://drive.google.com/drive/folders/1bQcgqPn_BAYNGlyCVrX_IRLDvYbQjf8t
I am wondering …
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I'm running the pipeline on a practice AshkenaziFam dataset before trying it on my own data. I'm having trouble getting the AshkenaziFam-ensemble.db file at the end of my run. Previously, I was runn…
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Hi Jim,
I'm attempting to run igv.js-jupyter in a FireCloud Jupyter Notebook. I'm using the example notebooks you provide and I get the 'IGV Browser not ready' message that does not resolve over ti…
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I run the BaseRecalibrator,and at fisrt it can good running,after a time,I got this error:
htsjdk.samtools.SAMFormatException: Invalid GZIP header
This is the log:
Using GATK jar /data/home/wuly/so…
wuuly updated
4 years ago
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Hello,
I'm running into issues with joint genotyping on 2500 (small) GVCF files. I'm running GATK4 from bcbio-nextgen on an SGE cluster and `GenomicsDBImport` runs into: `OSError: [Errno 7] Argumen…
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Hi,
I was testing the variants calling by deepvariant (DV) using PacBio CCS long reads https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_SequelII_…
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## Bug Report
I was running the JointDiscovery pipeline as a part of the GATK Best Practices pipeline. I am running this on many vcf files (~150) called by the HaplotypeCaller. I am getting this erro…
vymao updated
4 years ago
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Hello,
Since I saw this step uses only on core on my 20 core system, I searched on GATK forum and found this:
```
https://gatkforums.broadinstitute.org/gatk/discussion/23453/gatk4-baserecalibrator-…