homework_6_ancestry
Differences
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 16:13] scott /* Code for Homework */ |
||
|---|---|---|---|
| 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 = " | ||
homework_6_ancestry.txt · Last modified: 2015/11/16 10:18 by scott
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International
