Maria Asplund

We have looked at bcftools/sort and it looks like the md5sum of the zipped output vcf-file is different if you use a conda or docker profile. If you unzip the...

@FriederikeHanssen I was tagged by @asp8200 to look at this. We implemented a version of combining VCFs from structural variant callers before. We wanted to concatenate SV-calls from Manta, Cnvnator,...

Some comments: * My experience is that CNVkit works really bad without a reference dataset as it uses coverage distributions (log2ratios I think) to determine if something is out of...

@asp8200 Can you ad "VC=strelka" manually before the concat? Or is that to hacky?? :) Using svdb e.g. "set=delly" was added to the INFO field.

@asp8200 Maybe the best is to send the example to some "real" interpreters and see what they think :). With the risk of getting divergent replies :).

A suggestion for CNVkit (our users like it a lot), which is more work demanding though, is to have a CNVkit option where you add a reference .cnn file. https://cnvkit.readthedocs.io/en/stable/pipeline.html...