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I was testing `pipeline_v6.0` branch of `nf-core/oncoanalyser` in targeted mode. `purple` failed as below only for some of the samples. Same [issue](https://github.com/nf-core/oncoanalyser/issues/100)…
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Currently the package only supports human and mouse for the `species` parameter in `VJGeneTool.assign_vj_genes`. Since nanobody sequences are pretty common, have you considered adding support for alpa…
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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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How to incomplete/incorrect germline sets impact annotation?
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你好，
在文章方法的这一部分：
【Sequence annotation】
Variable regions, including FRs and CDRs were inferred using IgBLAST (Ye et al., 2013). Next, we numbered the gene sequences according to the IMGT numbering cr…
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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…
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I've encountered an issue where Monopogen appears to process multiple samples as a single sample during germline SNV calling, despite correctly handling them as separate samples in the preprocessing s…
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### Description of the bug
Joint germline genotyping completes actual genotyping, but fails at TSV count vcftools step
### Command used and terminal output
Command:
nextflow run nf-core/…
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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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### Description of feature
In order to deal with continuously growing number of gvcf files from haplotypecaller, it would be helpful to start the pipeline from the --joint_germline step. This would e…