[[annotation]]
file="ExAC.r0.3.sites.vep.tidy.vcf.gz"
fields = ["AN_Adj", "AC_Adj", "AN_Adj", "AC_AFR", "AN_AFR", "AC_AMR", "AN_AMR", "AC_EAS", "AN_EAS", "AC_FIN", "AN_FIN", "AC_NFE", "AN_NFE", "AC_OTH", "AN_OTH", "AC_SAS", "AN_SAS"]
names = ["in_exac_flag", "ac_exac_all", "an_exac_all", "ac_adj_exac_afr", "an_adj_exac_afr", "ac_adj_exac_amr", "an_adj_exac_amr", "ac_adj_exac_eas", "an_adj_exac_eas", "ac_adj_exac_fin", "an_adj_exac_fin", "ac_adj_exac_nfe", "an_adj_exac_nfe", "ac_adj_exac_oth", "an_adj_exac_oth", "ac_adj_exac_sas", "an_adj_exac_sas"]

ops=["flag", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self"]

[[annotation]]
file="ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz"
fields=["AF", "AMR_AF", "EAS_AF", "SAS_AF", "AFR_AF", "EUR_AF", "AF"]
names=["in_1kg_flag", "aaf_1kg_amr_float", "aaf_1kg_eas_float", "aaf_1kg_sas_float", "aaf_1kg_afr_float", "aaf_1kg_eur_float", "aaf_1kg_all_float"]
ops=["flag", "self", "self", "self", "self", "self", "self"]

[[annotation]]
file="clinvar_20150305.tidy.vcf.gz"
fields=["CLNSIG"]
names=["clinvar_pathogenic"]
ops=["self"]

[[postannotation]]
fields=["clinvar_pathogenic"]
op="lua:clinvar_sig(clinvar_pathogenic)"
name="clinvar_sig"
type="String"

[[annotation]]
file="cosmic-v68-GRCh37.tidy.vcf.gz"
fields=["ID"]
names=["cosmic_ids"]
ops=["concat"]

[[annotation]]
file="dbsnp.b141.20140813.hg19.tidy.vcf.gz"
fields=["ID"]
names=["rs_ids"]
ops=["concat"]

[[annotation]]
file="hg19_fitcons_fc-i6-0_V1-01.bed.gz"
columns=[4]
names=["fitcons_float"]
ops=["mean"]


[[annotation]]
file="ESP6500SI.all.snps_indels.tidy.v2.vcf.gz"
fields=["TAC", "EA_AC", "AA_AC", "TAC", "EXOME_CHIP"]
names=["in_esp_flag", "aaf_esp_ea_float", "aaf_esp_aa_float", "aaf_esp_all_float", "EXOME_CHIP_flag"]
ops=["flag", "lua:ratio(vals)", "lua:ratio(vals)", "lua:ratio(vals)", "flag"]

#[[annotation]]
#file="LCR-hs37d5.bed.gz"
#names=["LCR"]
#columns=[2]
#ops=["flag"]
#
#[[annotation]]
#http://humanparalogy.gs.washington.edu/build37/build37.htm
#  wget -O - http://humanparalogy.gs.washington.edu/build37/data/GRCh37GenomicSuperDup.tab \
#      | tail -n+2 \
#      | grep -Pv "_gl00|_random|chrUn" | sort -k1,1V -k2,2n | bgzip -c > GRCh37GenomicSuperDup.tab.gz
#file="GRCh37GenomicSuperDup.tab.gz"
#names=["superdup"]
#columns=[2]
#ops=["flag"]



[[annotation]]
file="encode.6celltypes.consensus.bedg.gz"
#chrom   start   end     gm12878 h1hesc  helas3  hepg2   huvec   k562
columns=[4,5,6,7,8,9]
ops=["concat","concat", "concat", "concat", "concat", "concat"]
names=[ "encode_consensus_gm12878", "encode_consensus_h1hesc", "encode_consensus_helas3", "encode_consensus_hepg2", "encode_consensus_huvec", "encode_consensus_k562"]

[[annotation]]
file="hg19.gwas.bed.gz"
columns=[4]
names=["gwas_pubmed_trait"]
ops=["concat"]

[[annotation]]
file="hg19.rmsk.bed.gz"
columns=[4]
names=["rmsk"]
ops=["concat"]

[[annotation]]
file="hg19.gerp.elements.bed.gz"
columns=[4]
names=["gerp_elements"]
ops=["mean"]

[[annotation]]
file="hg19.CpG.bed.gz"
columns=[2]
names=["cpg_island"]
ops=["flag"]

[[annotation]]
file="hg19.dgv.bed.gz"
columns=[4]
names=["dgv"]
ops=["concat"]

[[annotation]]
file="wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz"
columns=[4]
names=["tfbs"]
ops=["concat"]

[[annotation]]
file="genetic_map_HapMapII_GRCh37.gz"
columns=[4, 5]
ops=["mean", "mean"]
names=["hapmap1", "hapmap2"]


[[annotation]]
file="stam.125cells.dnaseI.hg19.bed.gz"
columns=[5, 6]
ops=["mean", "concat"]
names=["stam_mean", "stam_names"]

[[annotation]]
file="cse-hiseq-8_4-2013-02-20.bed.gz"
columns=[2]
ops=["flag"]
names=["cse-hiseq"]


[[postannotation]]
## a list of all fields required by the op below.
fields=["ac_exac_all", "an_exac_all"]
op="lua:div2(ac_exac_all, an_exac_all)"
name="exac_all_aaf"
type="Float"