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Added a data/hg19_to_GRCh37.chain for use with vcf2maf --remap-chain, to simplify lives of users handling hg19 VCFs. Notice how only chrM➜MT needs genomic loci remapping, while all others just need renaming.
Better handling of ExAC allele counts, without needing VEP's ExAC plugin. See #90, #91, #37 for details.
Now using ExAC subpopulation allele counts for FILTER tag common_variant, instead of allele frequencies.
So the common_variant tag is now redefined as: If allele count across at least one ExAC subpopulation (AFR AMR EAS FIN NFE OTH SAS) is >16, and ClinVar doesn't say it's pathogenic.
The maximum subpopulation allele count is also configurable with --max-filter-ac, defaulting to 16. The ExAC VCF can also be swapped out with the gnomAD VCF, when it's released, using argument --filter-vcf.