Genotyping
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Filtering by Variant Effect
- Eloise Valasek
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Gene mutations as a binary variable
- Sara Nofal
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SNP availability for known genes
- Helena Bird
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extract phased genotypes from "the definition of field 22438 bgen file"
- Yuandan Zhang
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Standard polygenic risk scores analysis
- Tamir Eisenstein
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Predicting genetic ancestry using the gnomad random forest model
- Megan R
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UKB ARP plink merge
- Wenqianglong Li
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SNP filtering error message
- Helena Bird
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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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