Go to the open bioinformatics site
Register for the annovar software and the link for the download will be sent to your email. Download the software to your computer you can also use the command "
wget link of the resource" to download the tool.
Unzip the folder
unzip ..
gunzip ..
Extract the .tar which is an archieve file
tar -xvf annovar.latest.tar
cd into the unzipped folder
move the scripts (.pl) in the folder to your bin folder
mv "file path and name" ~/bin/
Now, source your .bashrc
source /home/sam/.bashrc
enjoy annovar
The first thing to do after creating the repository online is to clone it to your HD
git clone link
check status with
git status
Addding online, use
git add
Commit will send to the intermediate cloud
git commit -m "message"
you need to push now to the microsoft cloud
git push -u origin master
online command
for i in README.md; do git add $i; git commit -m "first commit"; git push -u origin master; done
Editing vcf files (using txt file to select them and look for a location and print genotype at that location
for i in $(cat 2n3per_family.txt); do echo $i $(bcftools view --threads 10 -v snps -r chr13:20763294 "${i}.hard-filtered.gvcf.gz" | bcftools query -f '[ %GT]\n'); done
bcftools view -v snps -r chr13:20763294 all_samples_gh_20200422_joint_call.gvcf.gz | bcftools query -H -f '[ %GT]\n' | less -S
Sed programming is used above R is for a file with region yet a specific format is required
Using anaconda to install gatk
do
conda search gatk
look for your version to install
Install with the command below
conda install -c bioconda gatk=3.8
Download gatk from their website on your pc
unzip the gatk folder and cd into it
the gatk local .jar file with the gatk executable file (highlighted in blue) to your home bin
cp file name ~/bin/s