Advanced tools and tutorials
-
What is the best tool to apply Hardy-Weinburg Equilibrium filtering to find variants in a pVCF with a p-value > a given threshold (10^-15)?
- Permanently deleted user
-
dxfuse -limitedWrite on RAP?
- Permanently deleted user
-
BOLT-LMM v2.4 update for RAP
- Permanently deleted user
-
Are WES pVCF files (Data-Field 23148) already filtered for Genotype depth (SNV DP >= 7, INDEL DP>=10) and allele balance filters (hetzyg SNV AB >0.15, hetzyg INDEL<0.2)?
- Permanently deleted user
-
How to run VEP docker image using swiss-army-knife?
- Former User of DNAx Community_4
-
Using Tabix in Swiss-Army-Knife
- Former User of DNAx Community_88
-
Multiple job failures + data retention
- Former User of DNAx Community_69
-
What is the typical time taken to launch a JupyterLab instance? My regular instance (not Spark) has been in "Launching" state for the last 16 minutes. This seems like an excessive amount of time taken to launch. How long does this typically take?
- Former User of DNAx Community_70
-
How to export a matrix table as a VCF file after annotation on UKB RAP using HAIL?
- Former User of DNAx Community_4
-
If you want to run commands on many large files (such as whole-genome sequencing CRAM files), won't transferring the files to project storage take a lot of time/compute?
- Brenton Pyle
-
JupyterLab Spark SQL queries keep hanging
- Former User of DNAx Community_62
-
Is there an updated version of plink available with the Swiss Army Knife?
- Former User of DNAx Community_55
-
Why does VCFtools force the maximum allele filter to 2 on Swiss Army knife? This doesn't happen when running VCFtools outside of DNA Nexus.
- Former User of DNAx Community_46
-
Where I can find sample codes how to LiftOver genotype data from HG37 to HG38 using Picard LiftOverVCF?
- Permanently deleted user
-
Is there a way to view the spark UI when running jupyter notebooks?
- Former User of DNAx Community_55
-
Where is dxjupyterlab-vep on spark cluster with HAIL-VEP? Cache is not found either.
- Former User of DNAx Community_4
-
Unable to save Hail output files
- Former User of DNAx Community_66
-
Copying workflows within projects and copying ICD codes in cohort browser.
- Former User of DNAx Community_42
-
Attempt to retrieve all data fields from a cohort failed in dxjupyter notebook. I am wondering what the error means and the best practice for retrieving all fields for every participant may be.
- Former User of DNAx Community_26
-
Dear DNAnexsus team, Is it possible to turn the cohort browsers filters once a cohort has been generated into "code" for reproducibility/ more CLI orientated members of our team? Many thanks
- Former User of DNAx Community_45
-
Can "Swiss Army Knife" functionality be obtained on "Cloud Workstation"?
- Permanently deleted user
-
I run vcftools for multiple files, but when I use swiss army knife and use *, I get an error as it sees my input as extra arguments, instead of running it once for each file. Is there any way to avoid merging all the vcf files into one?
- Former User of DNAx Community_43
-
How I can export a Jupyter lab notebook as pdf of HTML. I go to File > Export > HTML or PDF but I keep getting an error that the page is not there.
- Permanently deleted user
-
Failed to visualize data
- Former User of DNAx Community_61
-
Hi! Question: How to retrieve all fields (from phenotypic data) for a specific sample or list of samples (provided a file for example)?
- Former User of DNAx Community_85
-
Should there be a pruning step in the REGENIE step1 workflow?
- Former User of DNAx Community_28
-
Is there any way (e.g., using samtools/htsget) to access a slice of cram file (corresponding to a single genomic region) on RAP without downloading the whole cram file to a compute instance?
- Permanently deleted user
-
How can I estimate the resources that an AWS instance used after a run?
- Former User of DNAx Community_48
-
App Building cheatsheet now available
- Ted Laderas
-
zcat output empty
- Former User of DNAx Community_85
Didn't find what you were looking for?
New post