Update Genotype vcf to rda process - Githubissues

LieberInstitute / goesHyde_mdd_rnaseq

Fernando Goes and Thomas Hyde MDD RNA-seq project

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Update Genotype vcf to rda process #16

Open lahuuki opened 3 years ago

lahuuki commented 3 years ago

With the new TopMed genotypes provided by @joshstolz, some of the steps in https://github.com/LieberInstitute/goesHyde_mdd_rnaseq/blob/def198e90fec5e6f3bf3e4b4d1c2bbea997ad467/genotype_data/pull_genotype_data.R and https://github.com/LieberInstitute/goesHyde_mdd_rnaseq/blob/def198e90fec5e6f3bf3e4b4d1c2bbea997ad467/genotype_data/pull_genotype_data_plink.R are now redundant. Need to remove the the MAF filtering and dbSNP matching steps.