Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.
Several places in the scripts make use of "magic numbers" and other shortcuts that mean that despite seeming to be general, they are highly tuned to the use of specific resource files.
It would be better to use an actual VCF parsing package (e.g. https://pyvcf.readthedocs.io/en/latest/) instead. The code will be cleaner and probably shorter as well.
Several places in the scripts make use of "magic numbers" and other shortcuts that mean that despite seeming to be general, they are highly tuned to the use of specific resource files.
It would be better to use an actual VCF parsing package (e.g. https://pyvcf.readthedocs.io/en/latest/) instead. The code will be cleaner and probably shorter as well.