Genotyping
Haplotypes and imputation
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Availability of APOE genotypes
- Michael Lutz
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Which Genotype Dataset in UK Biobank Is Most Comprehensive for PRS Calculation, and Can Training and Testing PRS Be Combined?
- Lu Ao
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Resolving Missing rsIDs in TOPMed Imputation Data for GWAS Analysis
- Sahar Mikaeeli
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prsice2 in CLI
- Wang Lei
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Query about bgen to vcf conversion time on UKB RAP
- Baozhuo Ai
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Liftover of SNP genotype calls GrCH387 to GRCH38 - why not just use rsids as recommended by UCSC?
- Gabriel Doctor
- Edited
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extracting allele combinations at specific SNPs
- Fatemeh Tabassi Mofrad
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Genotyping: merging .bed, .bim, and .fam files from array data
- Tamrat Befekadu Abebe
- Edited
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Run LD clumping, returned non-zero exit status 255.
- Shengcun Li
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Inquiry on QC and GWAS Pipeline
- Xiaomin
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plink --merge-list gives wrong chromosome annotations. GWAS tutorial.
- Robin Mjelle
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Map PRS score to EID
- Jinhan Zhu
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How do I extract allele combinations at specific SNPs using Jupyterlab?
- Renuka Devi Chintapalli
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Ancestry-specific PCs
- Saif Dababneh
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How to resolve REGENIE errors with GEL and TOPmed BGEN indices
- Mike
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Variants imputed or sequenced in BGEN file
- Former User of DNAx Community_13
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Availability of pre-computed relatedness information?
- Permanently deleted user
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Imputing UKB genotypes with HRC
- Former User of DNAx Community_39
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How can I exclude with participants have specific genotype from my cohort using cohort browser?
- Permanently deleted user
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How to deal with qctool Error: sample file and genotype file sample IDs do not match!
- Former User of DNAx Community_10
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I am trying to extract a specific snip from ukb22418_cMT_b0_v2 the mitochondrial hard called chromosome file, The snps are labeled with Affx-, not rs... How do I extract a specific snp, for example Affx-34461959. The usual plink command doesn't work
- Former User of DNAx Community_10
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incorporate some additional phenotype variables that are not included here: https://github.com/dnanexus/UKB_RAP/blob/main/end_to_end_gwas_phewas/get-phewas-data.ipynb
- Former User of DNAx Community_42
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Saige GWAS giving p value/se == 0 for top hits
- Former User of DNAx Community_6
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How to filter snpEff.vcf.gz file on UKB RAP?
- Permanently deleted user
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Can I use Haploview on DNAnexus
- Former User of DNAx Community_31
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gatk's GenotypeGVCFs always gives an error when analyzing full exon data of.g.vcf.gz form in UK biobank: The list of input alleles must contain < NON_REF> as an allele but that is not the case at position 68991;
- Former User of DNAx Community_66
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Where can I find the BWA Reference Genome Index file?
- Permanently deleted user
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Is the UKB going to provide the genotype array data and the imputed data in GRhC38 coordinates for general use in the platform? Given that the WES and WGS release are also in this coordinate system it would make sense. Thank you
- Permanently deleted user
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I am hoping I can have a script to run SAIGE GWAS on Dx command line using bgen files. Best- Nihal
- Former User of DNAx Community_91
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How to download selected genotyping data (CEL files)
- Former User of DNAx Community_11
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