Maxime U Garcia

Close issue that has been resolved already

Closing issue that should have been close in 2020 already

> @drpatelh Given this is 4 years old, I'm leaning towards closing it and asking oyu to start from scrach. > > Will give you a week to think about...

@combiz has this been fixed?

@apeltzer still noticing this issue?

> So here I ran deepvariant, mpileup, strelka and freebayes, and I get the same variant called three times: > > ``` > ##bcftools_concatCommand=concat --output testN.vcf.gz --threads 1 testN.deepvariant.vcf.gz testN.bcftools.vcf.gz...

Can you do a `nextflow run -r dev -latest ...`

or a `nextflow pull nf-core/sarek -r dev` before the `nextflow run ...` command

> So far I am just concatenating the germline-vcfs from haplotypecaller and strelka, and placing the resulting vcf `.germline.vcf.gz` in the results-folder `results/variant_calling/concat/`. I think it's best to start small,...

> I'd say that makes the text-file redundant, right? yes, that's enough for me indeed