homework_6_ancestry
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homework_6_ancestry [2015/11/13 17:51] scott |
homework_6_ancestry [2015/11/15 18:17] scott /* Code for Homework */ |
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| + | ==== Notes ==== | ||
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| + | ==== Code for Homework ==== | ||
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| # PSYC 7102 -- Statistical Genetics | # PSYC 7102 -- Statistical Genetics | ||
| Line 21: | Line 28: | ||
| ### ONLY EXPLAIN COMMANDS WHERE I SPECIFICALLY REQUEST IT! YOU DO NOT | ### ONLY EXPLAIN COMMANDS WHERE I SPECIFICALLY REQUEST IT! YOU DO NOT | ||
| - | ### HAVE TO EXPLAIN EVERY COMMAND! | + | ### HAVE TO EXPLAIN EVERY COMMAND! |
| + | ### in the end a PCA plot containing yourself compared to all 1000 Genomes | ||
| + | ### samples. | ||
| # For many questions you'll want to run analyses by chromosome. To do | # For many questions you'll want to run analyses by chromosome. To do | ||
| Line 28: | Line 37: | ||
| qsub -I -l walltime=23: | qsub -I -l walltime=23: | ||
| - | ### Load apigenome, plink, and R | + | ### Load apigenome, plink |
| module load apigenome_0.0.2 | module load apigenome_0.0.2 | ||
| module load plink_latest | module load plink_latest | ||
| Line 73: | Line 82: | ||
| ### Add in rsIDs from dbSNP. PLINK needs these to reconcile | ### Add in rsIDs from dbSNP. PLINK needs these to reconcile | ||
| ### positions/ | ### positions/ | ||
| - | vcf-add-rsid -vcf chrALL.filtered.PASS.beagled.HG00096.vcf.gz -db / | + | vcf-add-rsid -vcf chrALL.filtered.PASS.beagled.HG00096.vcf.gz -db / |
| ### The previous command keeps only variants with rsIDs, otherwise | ### The previous command keeps only variants with rsIDs, otherwise | ||
| ### plink throws an error that there are >1 variants with ID = " | ### plink throws an error that there are >1 variants with ID = " | ||
| Line 96: | Line 105: | ||
| ###------ QUESTION 2: WHAT DOES THIS COMMAND (THE ENTIRE FOR LOOP) DO? (2 points) | ###------ QUESTION 2: WHAT DOES THIS COMMAND (THE ENTIRE FOR LOOP) DO? (2 points) | ||
| for i in {1..22}; do | for i in {1..22}; do | ||
| - | zgrep -E ' | + | zgrep -E ' |
| done | done | ||
| ### 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 | + | ### |
| + | ###------ QUESTION 3: WHY WOULD WE RETAIN ONLY COMMON SNPS, OTHER THAN IT | ||
| ### | ### | ||
| for i in {1..22}; do | for i in {1..22}; do | ||
| Line 244: | Line 254: | ||
| R | R | ||
| ### Then in this R session run: ' | ### Then in this R session run: ' | ||
| - | ### If you log out and back in, you'll have to again run this command: | + | ### If you log out and back in, you'll have to again run this command |
| export R_LIBS=/ | export R_LIBS=/ | ||
| Line 261: | Line 271: | ||
| ### ' | ### ' | ||
| - | kg_sf <- read.table(' | + | kg_sf <- read.table(' |
| sample_ids <- unique(data.frame(IID=kg_sf$SAMPLE_NAME, | sample_ids <- unique(data.frame(IID=kg_sf$SAMPLE_NAME, | ||
homework_6_ancestry.txt · Last modified: 2015/11/16 10:18 by scott
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