| *bcftools filter | |
| *Filter variants per region (in this example, print out only variants mapped to chr1 and chr2) | |
| qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz | |
| *printing out info for only 2 samples: | |
| bcftools view -s NA20818,NA20819 filename.vcf.gz | |
| *printing stats only for variants passing the filter: | |
| bcftools view -f PASS filename.vcf.gz |
This guide assumes you're working on a Unix-like environment. I'm using Linux Mint (Ubuntu). It should work on Macs, and might on Windows.
These are the four steps you can use as a checklist, see the headings below for the details on each step.
~/.authinfo.gpg
| // ==UserScript== | |
| // @name Clean Pubmed Search Links | |
| // @namespace https://github.com/ndefrancesco | |
| // @version 1.0 | |
| // @author Nicolás De Francesco | |
| // @include https://pubmed.ncbi.nlm.nih.gov/* | |
| // @include http://pubmed.ncbi.nlm.nih.gov/* | |
| // @require http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js | |
| // ==/UserScript== |
Website: https://www.tidyverse.org/packages/
Comparison of dplyr and base functions: https://cran.r-project.org/web/packages/dplyr/vignettes/base.html
Piping:
library(dplyr)
| // ==UserScript== | |
| // @name Twitter Promoted | |
| // @namespace http://tampermonkey.net/ | |
| // @version 0.2 | |
| // @description Get rid of stupid promoted tweets | |
| // @author Mac Gaulin | |
| // @match http*://twitter.com/* | |
| // @grant none | |
| // ==/UserScript== |