genepi_ngs_scripts

Scripts, tools for working with next-generation sequencing data. For a very simple example of how to use my library in your own scripts, see sampleParse.py

best_practice_v4.sh, example.sh

BWA/GATK calling pipeline per GATK Best Practice v4. Options aren't yet comprehensive enough to cover the whole spec: for now, this assumes the "Best" post-processing strategy and uses hard filters (I only work with a few samples at a time).

To use this, you should make a copy of example.sh (named appropriately) for each run that you do, tweaking its parameters as needed.

This also makes use of:

• dpFilter.py: Per the Best Practice hard filters, a DP filter should be applied if the DP exceeds 5 or 6 sigma, but as far as I could tell, there's no utility to do this in GATK

• buildVAASTreference.py: This is a script that attempts to tweak the GATK bundle's .fasta reference genome to be compatible with VAAST (technically they give you the same reference genome, but I'm OCD :) ). As VAAST is still under heavy development, this works only about half of the time.

• removeAlternateContigs.py: For VAAST compatibility, strips out variants in a .vcf file that are not in chromosomes 1-22,X, or Y

vcfCleaner.py

A GUI front end to scripts that can manipulate/clean the results of the pipeline. The GUI is not quite ready, but each script can run independently:

• sort.py: Should be run on any file that is to be fed to any of these other scripts (sorts chromosomes, positions in 1-22,X,Y. All other chromosomes (chrUn, MT, etc) come after in alphabetic order)

• addBEDtoVCF.py: Adds per-feature scores in a .bed file to every intersecting variant in a .vcf file

• addCSVtoVCF.py: Adds per-variant scores in a .csv file to every variant in a .vcf file; supports three modes for matching rows: exact match, nearest neighbor, and interpolation

• calcStats.py: Really does two things: creates additional/alternate allele orderings, and calculates additional statistics for those allele orders

• cleanVCF.ph: Removes INFO fields from a .vcf file with an excessive number of categorical values

• filterVCF.py: Filters rows of a .vcf file per Python-syntax expressions

• VCFtoCVF.py: Converts a .vcf file to a .cvf file

• VCFtoCSV.py: Converts a .vcf file to a .csv file