Genotyping
Haplotypes and imputation
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Where can I find the BWA Reference Genome Index file?
- Permanently deleted user
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extracting allele combinations at specific SNPs
- Fatemeh Tabassi Mofrad
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Imputing UKB genotypes with HRC
- Former User of DNAx Community_39
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Availability of pre-computed relatedness information?
- Permanently deleted user
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Availability of APOE genotypes
- Michael Lutz
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How to filter snpEff.vcf.gz file on UKB RAP?
- Permanently deleted user
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I want to run a PheWAS analysis using PHESANT and currently trying to generate the phenotype file. I am using table exporter to extract the phenotype data for my variables of interest.
- Former User of DNAx Community_28
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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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I want to locate the pVCF UKB23352_c19 file that has position chr19:17642033-17642056. There are 1000 files. How do I do it?
- Former User of DNAx Community_10
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SNP filtering error message
- Helena Bird
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How do I extract allele combinations at specific SNPs using Jupyterlab?
- Renuka Devi Chintapalli
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Saige GWAS giving p value/se == 0 for top hits
- Former User of DNAx Community_6
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Saving files created with Rstudio
- Former User of DNAx Community_56
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Effectively querying genotypes from the Spark genotype table
- Former User of DNAx Community_22
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Run LD clumping, returned non-zero exit status 255.
- Shengcun Li
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Ancestry-specific PCs
- Saif Dababneh
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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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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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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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Genotyping: merging .bed, .bim, and .fam files from array data
- Tamrat Befekadu Abebe
- Edited
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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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Variants imputed or sequenced in BGEN file
- Former User of DNAx Community_13
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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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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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Cohort Browser geno filters high impact variant with OR
- Former User of DNAx Community_30
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If I do not see the BIM, MAP, FAM files on my approved database, does this mean that I do not have access to genotype results of chromosomes 1-22?
- Former User of DNAx Community_91
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