flaviaerius

View

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

Printing variants without header:

bcftools view -H

flaviaerius

Render Quarto with docker

Follow the steps below to set up a docker environment with RStudio to render your Quarto documents (.qmd). It allows you to knit Rmd documents too.

You should follow all steps exactly in the order they appear here, otherwise it may not work.

# In the terminal, get to the directory that contains your Rmd or quarto document and the files needed,
# and run the below command

flaviaerius

Install samtools, bcftools, htslib, bedtools, and plink2 on linux

Install some build dependencies

sudo apt update

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev wget libncurses5-dev bzip2