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Hi,
When I run the tool wham using the command
toolPath -e $EXCLUDE -f $reference -t $alignments | perl ${utilsPath}/filtWhamG.pl
The tool runs without any error with a non-zero runtime. Howeve…
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log:
```
2018-02-14 09:30:18,372 ERROR Command 'quantify /tmp/hap.py.result.jryogM.vcf.gz -o /mnt/yard2/ian/structural_variants/CHM1_CHM13_analysis/HG2.happy.roc.tsv -r /mnt/opt/refdata_new/hg1…
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For a better preview, we could separate each part of the text with code blocks.
for example in https://github.com/usegalaxy-eu/galaxy-social/pull/122 it could be something like this:
👋 Hello! I'm …
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Hello,
I'm also keen to integrate into the genome graph the structural variability detected by Sv callers (from short reads and/or long-reads). I was wondering if minigraph handles that?
Those are …
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`):
1.2.3
- OS name and version (`lsb_release -ds`):
CentOS release 6.9 (Final)
**To Reproduce**
```
bcbio_nextgen.py -n 16 sample…
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GDC: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
- features we'd like to support: snv, indel, structural variants, extra chromosomal dna
- create ta…
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Hi,
I am trying to run mtdna server by installing it offline, however i am using nextflow first time. i am able to install the process but encountered with the error:
ERROR ~ Unable to parse con…
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Good morning, I wanted to ask for some guidance regarding an issue I've been running into while genotyping structural variants using graphtyper. I am attempting a test-run of graphtyper v2 on multiple…
ghost updated
3 months ago
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- [x] BAM Generation and Quality Control : ACCESS_pipeline.cwl (ACCESS-Pipeline/workflows/)
- [ ] Small Variants: snps_and_indels.cwl (ACCESS-Pipeline/workflows/subworkflows/)
- [x] Copy Number Vari…
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Hello Fritz,
We have a tree genome pedigree in which we are comparing 5 different genomes to the reference genome. We aligned each genome using mummer4 and called structural variants. Now, we want …