This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
homework_6_ancestry [2015/11/14 10:16] scott |
homework_6_ancestry [2015/11/15 17:41] scott |
||
---|---|---|---|
Line 2: | Line 2: | ||
==== Notes ==== | ==== Notes ==== | ||
- | 11/14/2015 N.B.: Chelsie noted that the < | ||
Line 29: | 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 81: | 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 108: | Line 109: | ||
### 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 |