-
See this suggestion by @wm75: https://github.com/galaxyproject/iwc/issues/96
-
Hi
we have been trying to use SAIGE for single variant associations on a binary trait. The fit of a null logistic mixed model ("step 1") runs successfully but the single variant association test ("st…
-
In the below example, there are three SNPs that are non-polymorphic in the given set of samples, but these SNPs do not seem to be filtered out by the `min_maf = 0.05` argument in `SnpArrays.filter`. I…
-
Hi Kishwar,
I have just tested PEPPER Nanopore variant calling workflow. My result= is as follows：
##fileformat=VCFv4.2
##FILTER=
##FILTER=
##FILTER=
##FILTER=
##FILTER=
##FORMAT=
##FORMA…
-
Hi again,
I am running pileupCaller with -p POP enabled but I get the following error
Invalid option `-p'
Did you mean one of these?
-h
-d
-f
-e
The same if I use: --plin…
-
**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.3/docs/FAQ.md**: Yes
**Describe the issue:**
The error arises during the "postprocess_variants" step. The quick-test and a…
-
Hello,
First, apologies for the generic title, I wanted to leave it open-ended as I think I have various questions and maybe more when you've replied the existing ones.
Second, my compliments on…
-
I only want to save one variant possessed the best calling qulity from spanning alleles，how to batch process it？ thanks~
![image](https://user-images.githubusercontent.com/54714639/146139559-b73640d…
-
When using the Dragen and Allele Specific Annotation pipeline, what is the expected Ts/Tv ratio for the resulting PASSed call set. Previously the Ts/Tv is expected to be near 2.15 range. Is this expec…
-
The latest pangolin/PLEARN/Constellations files are producing likely erroneous AY.4.2 lineage calls for sequences collected Jan - Feb 2021. Scorpio call for these lineages is "Epsilon (B.1.427/429-li…