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hey,
How does this filter work?
`delly filter -f germline -o germline.bcf merged.bcf`
What criteria it uses?
With some set of samples I get no output, so I wonder if I could write my own filt…
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Hi,
Thanks for developing this nice tool.
I have called somatic `SNP/indel/SV/5mc`, then I want to phase somatic SNP/indel/SV/5mc. I also called germline SNP variants by Clair3, and then how to …
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Hi, I am trying to run Germline on the example provided in the repository. After successfully running preProcess, I run the following command:
python src/Monopogen.py germline -a apps/ -t 1 -r tes…
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Curate test data sets on AWS, preferably on S3 open data, this may include, germline, tumor/normal, genotype, RNASeq data.
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Hi,
I've put into a separate assets data needed to run germline analysis for Homo sapiens here : ~~https://github.com/apraga/human_genome_assets~~ https://github.com/apraga/germline_analysis_vep
D…
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I'm using the example data from the documentation.
In v1.6.0 - the file `chr20.germline.vcf` does not get generated from the germline calling step.
```
${path}/src/Monopogen.py germline -a ${pa…
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Hello,
I am using the Whole Genome Germline Single Sample workflow for big WGS experiments. I notices that the task of sorting bam after MarkDuplicates is consuming from 60% to 80% of the execution …
eprdz updated
2 weeks ago
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Hello all,
Thank you for making this great tool. In the example, the germline caller is used for chromosome 20 only. If we wish to perform germline calling for chromosomes 1-22 for a single sample,…