I am posting Useful Bioinformatics scripts here that I find useful.

##vcf_cutoff_stats.R This is an R script to calculate some different statistics related to depth and quality of vcf_files. Of course, this is not very specific and can be ported easily to other applications. This is not the most efficient script...; however, the R part is not the inefficient part. I believe the cat part into the this scirpt is the inefficient part. note tested with small fruitfly genome; your results may vary

#typical use case:
vcftools --site-depth --vcf your.vcf --out site_depth
vcftools --site-quality --vcf your.vcf --out site_quality

#outputs site_depth.ldepth and site_quality.lqual
#then pipe this output to the script

cat site_quality.lqual | vcf_cutoff_stats.R > vcf_quality_summary.txt
cat site_depth.ldepth | vcf_cutoff_stats.R > vcf_depth_summary.txt

#reference.fa.filter.py Stephen A. Sefick July 15, 2016

Use this script to remove sequences from a

fasta file that match a supplied pattern

#example usage:

./reference.fa.filter.py ">Unknown" dp4.fa.masked out

#">Unknown" is the pattern

#dp4.fa.masked is the reference genome

#out is the outfile