-
I ran Canvas Germline-WGS for several samples and all have lots of LOH variants (I consider only PASS variants.) For example, Illumina's .SV.vcf.gz for a sample has only one LOH:
16 GAIN
1 LOH
17 L…
-
### Description of the bug
I've run into an issue running the Sarek pipeline with Sea Urchin genome data. I would like to run Manta to find all variants from short read DNA sequencing data. I have al…
-
Thanks a lot for this great tool. I have some puzzles wanting for help
1 Can it be used for somatic
2 can it call EGFR or other genes complex variants
-
### Description of the bug
When I use my custom reference, error always show: This path is not available within annotation-cache. Please check https://annotation-cache.github.io/ to create a request …
-
Hi,
(Is it better to post this here or in the google group? As I'm not sure this is an issue, rather an operator error)
We have a project in which we want to include both germline and tumor sample…
-
For normal-tumor sample pair, when I run with somatic mode, I got a somatic variant in which normal variant allele frequency was 0.0526.
1 241680511 . T TA . PA…
-
We need to review what https://nf-co.re/sarek can do to determine:
- if it could be used as is
- if it could be used with modifications
- if we'd rather extract and replicate some functionality h…
-
Der Datensatz https://pub.h-brs.de/5398 enthält im Titel den Begriff "E-cadherin". Wenn man nur nach dem Begriff sucht, wird der Datensatz erwartungsgemäß gefunden, egal ob man ihn als Phrase mit Anfü…
-
With #754 we're halfway to also supporting inframe indels so we should just do the rest of the work necessary to support those types of proximal variants.
-
**Is your feature request related to a problem? Please describe.**
In a validation of the GMS Lymphoid panel there's been a few variants in the reference samples that were filtered out in the VCF d…