###Download STAR### Obtain STAR source from https://github.com/alexdobin/STAR
Add the following to your .bashrc file and source it:
export PATH=/path/to/STAR/bin/:$PATH
###Generate Reference Genome
#!/bin/bash | |
# function Extract for common file formats | |
function extract { | |
if [ -z "$1" ]; then | |
# display usage if no parameters given | |
echo "Usage: extract <path/file_name>.<zip|rar|bz2|gz|tar|tbz2|tgz|Z|7z|xz|ex|tar.bz2|tar.gz|tar.xz>" | |
else | |
if [ -f "$1" ] ; then | |
NAME=${1%.*} |
###Download STAR### Obtain STAR source from https://github.com/alexdobin/STAR
Add the following to your .bashrc file and source it:
export PATH=/path/to/STAR/bin/:$PATH
###Generate Reference Genome
FROM python:3.6-slim-stretch | |
ADD requirements.txt /tmp/requirements.txt | |
RUN apt-get update && \ | |
apt-get install -y \ | |
build-essential \ | |
make \ | |
gcc \ | |
locales \ |
# Source: https://stackoverflow.com/a/43317244 | |
$path = ".\aws-ec2-key.pem" | |
# Reset to remove explict permissions | |
icacls.exe $path /reset | |
# Give current user explicit read-permission | |
icacls.exe $path /GRANT:R "$($env:USERNAME):(R)" | |
# Disable inheritance and remove inherited permissions | |
icacls.exe $path /inheritance:r |
*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 |
name: CI | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main |