scripts for genetics

Bash scripts and other stuff I always google

Category	Description	Author
simple genetics bash scripts	vcf.gz commands	Seb
bcftools	vcf.gz commands	Seb
docker	basic docker commands	Seb
realign	realign BAM file	Seb
imputation	prepare data for Michigan Imputation Server	Seb
chip-data	create vcf files from Illumina data	Seb
1GP3	download 1000 Genomes lpa data	Hansi

Extract zips with passwords (e.g. from MIS)

Save script in same folder as zips and run with ./script.sh

#!/bin/bash
for FILE in *.zip;
do 7z x -p"$1" $FILE;
done

Delete all Docker containers

 docker rm -vf $(docker ps -a -q)

Delete all Docker images

  docker rmi -f $(docker images -a -q)

Replace SPACE with TAB

sed -e 's/ /\t/g' <in> > <out>