Genotyping
Haplotypes and imputation
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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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Effectively querying genotypes from the Spark genotype table
- Former User of DNAx Community_22
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Saving files created with Rstudio
- Former User of DNAx Community_56
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Cohort Browser geno filters high impact variant with OR
- Former User of DNAx Community_30
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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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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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How to store large genotype/phenotype data on the RAP that will be queried within custom code?
- Former User of DNAx Community_21
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What is the best way to label loss-of-function variants to then perform GWAS on LoF variants and phenotypic outcome? Would a SnpEff -> SnpFilt -> Plink2 pipeline make sense? I am new to this type of research!
- Permanently deleted user
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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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Where can I access to the codes used in the webinar " GWAS on Research Analysis platform using Regenie"?
- Permanently deleted user
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