This readme.txt describes and summarizes the files in the vt resource bundle.

Files are based on hs37d5.fa made by Heng Li.

data set (bcf)                samples    snps/indels/complex/sv/trs      description 
1000G.v5                      0          81316694/3296894/66806/59426/0  1000G v5. [1000G 2015?]
dbsnp138                      0          10588965/2488793/69749/0/0      derived from GATK's resource bundle that excludes 1000G variants.
1000G.omni.chip               2141       2432554/5/0/0/0                 1000G individuals typed on the omni chip [1000G 2015?]
mills                         0          0/208753/0/0/0                  indels from [Mills 2006]
mills.chip                    158        0/8904/0/0/0                    indels from [Mills 2011]
affy.exome.chip               2122       281875/34389/0/0/0              1000G individuals and others typed on the affymetrix exome chip [1000G 2015?]
NA12878.broad.kb              1          281345/87389/152/0/0            from GATK's NA12878 knowledgebase.
NA12878.v7.illumina.platinum  1          3702969/650764/13751/0/0        Illumina's platinum genomes version 7
NA12878.v8.illumina.platinum  1          3776096/692955/3910/0/0         Illumina's platinum genomes version 8
NA12878.nist.giab.v2.19       1          2787294/363036/2098/0/0         NIST Genome In a Bottle v2.19
UK10K.20140722                0          42415506/4198841/0/0            UK10K variants
codis                         0          0/0/0/0/15                      CODIS STRs plus 2 Pentanucleotide repeat STRs from Promega

file (bed.gz)          description 
mdust                  regions of low complexity annotated using mdust [Morgulis 2006]
rmsk                   repeat regions from repeat masker obtained from UCSC genome browser HG19 database
gencode.v19.cds        coding sequence regions based on GENCODE v19 annotations [Harrow 2012]
trf.lobstr             tandem repeat finder STRs (motif length 1 to 6) from lobSTR's resource bundle [Gymrek 2012]
trf.vntrseek           tandem repeat finder STRs (motif length 7 or more) from VNTRseek's resource bundle [Gelfand 2014]

Note:  Please let me know if I did not cite a resource properly.

maintained by: Adrian Tan (atks@umich.edu)