The utility of this pythons script is to filter variants out of a VCF based on the call rate of the genotypes.
Example: A VCF has hundred samples. There are 10000 variants in the VCF with genotypes for every sample. The script counts the number of genotype calls and no calls present in the genotypes and then calculates call rate as follows
Call Rate = No. of called genotypes (0/0, 0/1, 0/2, 1/2, etc and not ./.) / Total number of genotyes (2 x number of samples)
Based on the user provided cutoff, a variant will be filtered out if the call rate is less than the user input.
Usage:
python vcf_callratecheck.py input.vcf cutoff
Output: The script creates a VCF file with variants that passed the thresold and a log file in the format of a VCF with variants that failed to pass the thresold.