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Hello,
Operatin system: Linux HPC
Version: 1.3.0
Installation: Singularity
Data: WES - with Agilent SureSelect DNA Human All ExonV5_hg38 bed file
**Steps to reproduce:**
**Command**
```
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## Bug Report
### Affected tool(s) or class(es)
ReblockGVCF
### Affected version(s)
- [x ] Latest public release version [version?] _**GATK 4.2.6.1**_
- [ ] Latest master branch as of [date o…
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Hello,
I'm trying to debug my installation of the singularity GPU version for a new C4140 GPU node with Tesla V100s. I've run the CPU version successfully in production and am very happy with it, b…
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The command I use is as follows:
run_clair3.sh \
--ref_fn=/home/gyc/ont/seq/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
--bam_fn=/home/gyc/ont/fast5/workspace/output/out166/std/out.bam \
--t…
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Hi, I was trying to have a VCF related workflow, which involves gatk4, picard tools.
As an example, lets say I want to call gatk4 first to get some VCF files, and use picard to sort them.
if i h…
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I used StrelkaGermlineWorkflow to call variants using RNA seq data. Then I used following commands to check this file:
```
bcftools norm -m +any -O z -o unmarked.vcf.gz NoMarked.vcf.gz
```
thi…
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#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify.
(ru…
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## This section is required for PM/ADAPT team
### [Required] For what study (study_id) is this request?
OpenPedCan
### [Required] Basic study information
- [x] Is this an OT or Kids F…
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# Problem overview
In `tbpore`, we downsample the reads depth to 150x and we have a lower bound for the phred-scaled VCF call quality of 85 (which accepts only 1 error in 100M - this is an oversimp…