##Purpose Various scripts that compare variants between VCF files. Variant comparison files and statistics are produced.
vcf_compare.py: Compares any number of VCF files.
vcf_compare_inheritance.py: Additionaly analyzes inheritance. (Use with VCF files obtained from a parent-offspring trio.)
vcf_compare_exact_same.py: Compares VCFs expected to be exactly the same as each other. (e.g., the same sample run through different Galaxy instances, but processed identically otherwise.)
##Requirements Python 2.x (https://www.python.org/)
PyVCF (https://github.com/jamescasbon/PyVCF)
matplotlib (http://matplotlib.org/)
##Example commands
python vcf_compare.py a.vcf b.vcf --out_stats c.html --out_all_variants d.txt --out_absent e.txt --out_multiple f.txt --min_qd 5 --min_qual 100 --min_dp 20
python vcf_compare_inheritance.py -p1 a.vcf -p2 b.vcf -c c.vcf --out_stats d.html --out_all_variants e.txt --min_qd 5 --min_qual 100 --min_dp 20 (Where c is the child in a trio, p1 is Parent 1 and p2 is Parent 2.)
##Contact Julie Wertz (julie-wertz@uiowa.edu)