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homework_6_ancestry

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homework_6_ancestry [2015/11/15 23:13] – /* Code for Homework */ scotthomework_6_ancestry [2015/11/16 17:18] (current) – scott
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 module load apigenome_0.0.2 module load apigenome_0.0.2
 module load plink_latest module load plink_latest
 +module load tabix_0.2.6
  
  
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 ### Retain in the 1000 Genomes VCF only your SNPs that are also fairly common ### Retain in the 1000 Genomes VCF only your SNPs that are also fairly common
-### +### because we're going to conduct PCA on these SNPs and only want common ones. 
-###------ QUESTION 3: WHY WOULD WE REMOVE COMMON SNPS, OTHER THAN IT+###  
 +###------ QUESTION 3: WHY WOULD WE RETAIN ONLY COMMON SNPS, OTHER THAN IT
 ###------             MAKES EVERY COMMAND LATER FASTER? (2 points) ###------             MAKES EVERY COMMAND LATER FASTER? (2 points)
 for i in {1..22}; do for i in {1..22}; do
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 ### 'Self-reported' ancestry of 1000g participants ### 'Self-reported' ancestry of 1000g participants
-kg_sf <- read.table('/Users/scvr9332/20130502.sequence.index', header=T, sep='\t', fill=T, stringsAsFactors=F)+kg_sf <- read.table('/Users/scvr9332/PCA/20130502.sequence.index', header=T, sep='\t', fill=T, stringsAsFactors=F)
  
 sample_ids <- unique(data.frame(IID=kg_sf$SAMPLE_NAME, POPULATION=kg_sf$POPULATION, stringsAsFactors=F)) sample_ids <- unique(data.frame(IID=kg_sf$SAMPLE_NAME, POPULATION=kg_sf$POPULATION, stringsAsFactors=F))
homework_6_ancestry.1447629200.txt.gz · Last modified: by scott