mutect dbsnp file gotchas

[timodonnell]

Just noting this in case it matters later, regarding the dbsnp_alt_url and dbsnp_broad_url defined here to be passed to mutect:

https://github.com/hammerlab/biokepi/blob/master/src/lib/run_environment.ml#L656-L657

• the dbsnp_alt_url is a dead link: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/v4.0/00-All.vcf.gz
• I think a copy of that file is available here: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/VCF/00-All.vcf.gz
• however, dbsnp_alt_url and dbsnp_broad_url are not the same files. The broad URL gives a VCF with 61M records; the alt url gives one with 145M records.