arupgsh

# 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

arupgsh

*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

arupgsh

#!/usr/bin/env python
# numpy and biopython are required -- pip install numpy biopython

from Bio import Entrez
from Bio import Medline

MAX_COUNT = 10
TERM = 'Tuberculosis'

print('Getting {0} publications containing {1}...'.format(MAX_COUNT, TERM))