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Working with Hail outside of JupyterLab
- Former User of DNAx Community_41
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Efficient ways to use Swiss Army Knife
- Former User of DNAx Community_56
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ConnectionPoolTimeoutException while working in JupyterLab
- Former User of DNAx Community_41
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Tools tab not showing RStudio as an option?
- Former User of DNAx Community_57
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Using PLINK GWAS tool on the RAP generates a text output file with many duplicates. How do I get rid of the duplicates?
- Former User of DNAx Community_10
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When running dx download within an applet does this incur an egress fee? (data downloaded from project applet is running in) Many Thanks, Barney
- Former User of DNAx Community_51
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I used RAP tool to do a PLINK GWAS but results did not include X or XY files, only 22 autosomes. How do I include X and XY chr files.
- Former User of DNAx Community_10
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How can I get data from a DNA Nexus database into another format?
- Former User of DNAx Community_47
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Where does saved data go on a Jupyter spark cluster?
- Former User of DNAx Community_47
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How to submit a large input-json with dx run?
- Former User of DNAx Community_18
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Will there be UKB WGS PLINK bfiles?
- Former User of DNAx Community_4
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Effectively querying genotypes from the Spark genotype table
- Former User of DNAx Community_22
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I am wondering if there is any way/software on DNAnexus platform to call somatic mutations on UKB data?
- Former User of DNAx Community_19
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Extract multiple regions from CRAM with samtools view on the RAP
- Permanently deleted user
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Are UKB pVCF wes files truly bgzipped?
- Former User of DNAx Community_22
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ExecutorLostFailure when trying to write a matrix
- Former User of DNAx Community_22
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The sample code to load a VCF file with Hail is failing for me when I try it on a single 6 Gb VCF from the whole genome pVCFs. Can you help me to resolve this error?
- Former User of DNAx Community_47
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JupyterLab Server Connection Error
- Former User of DNAx Community_41
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What is the best way to separate participant IDs by ancestral genetic grouping? Similar to Data-Field 22006 (Genetic ethnic grouping) but for each ancestral group and not just Caucasians.
- Permanently deleted user
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How to locate a region of interest within a chromosome while there are multiple pVCF files for that chromosome (WES data)?
- Former User of DNAx Community_23
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How to create an applet which uses spark and a custom docker image
- Former User of DNAx Community_8
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Saving files created with Rstudio
- Former User of DNAx Community_56
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200K WGS pVCF on RAP
- Permanently deleted user
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What is the best way to run custom python script to analyze exome data?
- Former User of DNAx Community_57
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What is the best way to filter samples to keep only unrelated individuals as well as only one individual from related pairs? I am working with WES pVCF files.
- Permanently deleted user
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material for the Reproducible Research Using Docker webinar
- Chai Fungtammasan
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Hello, When looking at a specific variant in a cohort in the Genomics tab, is it possible have access to IDs of the patients having this specific variant ? Thank you !
- Former User of DNAx Community_74
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OS on the computing servers?
- Permanently deleted user
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WGS cram files truncated?
- Permanently deleted user
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I submitted a batch of 500 jobs to UKB/RAP. The number of running jobs is always 100 and the rest in waiting. Is this defined by UKB/RAP, or is it changeable?
- Permanently deleted user
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