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Hello, I am wondering if it's possible to input a script into swissarmyknife instead of individual commands? If so, how would I do this?
- Former User of DNAx Community_37
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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
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Hello, If I am looking to create a dataframe of around 200,000 participants, with individual nucleotide information regarding around 20 SNPs, what is the best way to go about doing this? Thanks :)
- Former User of DNAx Community_37
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Hi folks, I have a basic question for you?how can we access the exome sequencing data (preferably as the VCFs) using HAIL on the UKB RAP?
- Former User of DNAx Community_7
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Combining genotype data with phenotype data in Rstudio workbench
- Former User of DNAx Community_40
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I want to liftover the genotype array calls from hg37 to hg38. I reviewed the DNAnexus liftover GitHub but I am still unsure how to perform the liftover.
- Former User of DNAx Community_28
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I am performing QC as per the AD-by-proxy-GWAS guide. For this, I need to load the WES files into my JupyterNotebook but I keep getting an error.
- Former User of DNAx Community_28
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How do I filter a particular exome SNP rsID for a particular EID?
- Former User of DNAx Community_3
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Best way to perform Hardy-Weinberg Equilibrium filtering on WES pVCF on the RAP? Can I rely on the 'Ethnic Background' (Data-Field 21000) data field for delineation of populations?
- Permanently deleted user
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What's the best way to find allele frequency for a variant in the WES data?
- Former User of DNAx Community_28
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When I generate a new file in a JupyterLab notebook and upload it to my project storage, I cannot access that file in the same session, even if I refresh. I get the error that the file does not exist.
- Former User of DNAx Community_13
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How to merge VCF files with Swiss Army Knife?
- Former User of DNAx Community_56
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I'm having difficulty install the R package devtools, has anyone else had success installing this package?
- Former User of DNAx Community_13
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dxfuse -limitedWrite on RAP?
- Permanently deleted user
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BOLT-LMM v2.4 update for RAP
- Permanently deleted user
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Best practices for backups on RAP?
- Permanently deleted user
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Best way to run the same command on all CRAM files?
- Permanently deleted user
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How to use dxFUSE style file paths in Swiss Army Knife?
- Permanently deleted user
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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
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In a workflow, how to not upload intermediate files and only upload the output of the final step?
- Former User of DNAx Community_12
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Does anyone have a good tutorial on Eigensoft for use in DNAnexus?
- Former User of DNAx Community_33
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UK Biobank Cohort Update with Dataset Refresh
- Permanently deleted user
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How to run VEP docker image using swiss-army-knife?
- Former User of DNAx Community_4
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Best way to view a full VCF file?
- Permanently deleted user
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Using Tabix in Swiss-Army-Knife
- Former User of DNAx Community_88
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Webinar Sept 27: Analysis of Accelerometer and Metabolomic Data in the UK Biobank Dataset
- Brenton Pyle
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Is it possible to run Regenie step 2 with whole genome data rather than whole exome data considering that it is in pVCF format and there are more than 1 file for each chromosome?
- Permanently deleted user
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Is there a way to designate exclusions of participants whose genetic sex (DF: 22001) does not match their reported sex (DF: 31) within the cohort browser?
- Permanently deleted user
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