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Analyze.cosmic_fit(samples='/autofs/bal34/okwong/cancer_stat_proj/SigProfiler/lab_data',
output="/autofs/bal34/okwong/cancer_stat_proj/SigProfiler/lab_data/lab_data_test_GRCh37_100…
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I'm not familiar with snpeff and filter snv
i try
```
java -jar snpEff.jar databases|grep gnomad
```
i can't found anything
mabey i should[ build database](http://pcingola.github.io/SnpEff/s…
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I'm dropping here a user question/request from the customer support ticket ([#372436](https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=51204)):
Pertaining to the issue of SVs an…
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HaplotypeCaller
Call germline SNPs and indels via local re-assembly of haplotypes
Overview
The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplot…
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@mbabadi has some python scripts that we can expand upon. To start, this should include:
- [ ] WES evaluations using matched WGS as GT
- [ ] WGS evaluations using consensus calls from SV callers …
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The VCF spec contains this text on ALTs:
> Options are base Strings made up of the bases A,C,G,T,N,\*, (case insensitive)
or an angle-bracketed ID String (“\”) or a breakend replacement string as …
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Can you provide convenient commands for execution?
Such as
```
git clone https://github.com/broadinstitute/DirectHRD
cd DirectHRD
pip install -r requirements.txt
python download_deps.py
pytho…
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child of #3
arkal updated
6 years ago
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### Description of feature
Could be good to do whatever can be done when we release to help prepare for validation.
I'm thinking benchmarking, GiAB, checking results...
Could be interesting to talk…
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Hello! I'm trying to annotated a VCF file produced by CNVkit, using the latest conda version of AnnotSV:
`AnnotSV -SvinputFile /scratch4/nsobrei2/ggama1/somatic_SVs/cnvkit/vcfs/results/file.vcf -an…