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Sorry,
raredisease pipeline works for `germline` or `somatic` mutations? Can be used when there is no normal sample available (`tumour only mode`)?
Is any restriction for depth of coverage?
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Hi,
Thank you for this great tool.
I have a question with regard to SNV calling in paraloguous regions for WES/WGS illumina models.
As i understand, by default, candidates variants in regions with …
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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,…
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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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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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Hi I have list of 10X SingleCell data which R1 are missing from fastq files,
is there any way than we can align the R2 only using star and then feed bam file to monopogen germline
Thanks
should I u…
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I am calling CNVs in tumour ONT long-reads and want to try using spectre
I assume it is preferred to input SNPs from a matched tumour sample rather than germline SNPs? Or would germline SNPs be mor…
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Hi! Dr. Dou,
Thank you for developing this great software Monopogen for both germline and somatic SNVs detection in single-cell sequencing data. We found it very efficient in somatic mutations call…