423772af6e63fd93b062a3fb2e58151e92ca5bd1
angie
  Thu Sep 20 10:23:21 2012 -0700
Track #8886 (Denisova high-cov): Added composite track from Denisovaanalysis: sites where humans have a derived allele relative to chimp,
gorilla, and/or orangutan, and Denisova had the ancestral allele;
plus VEP annotations of predicted functional consequence.

diff --git src/hg/lib/dhcHumDerDenAnc.as src/hg/lib/dhcHumDerDenAnc.as
new file mode 100644
index 0000000..5258a38
--- /dev/null
+++ src/hg/lib/dhcHumDerDenAnc.as
@@ -0,0 +1,27 @@
+table dhcHumDerDenAnc
+"Human Derived, Denisova Ancestral variants and functional effect predictions from high-coverage Denisova sequencing project"
+    (
+    string chrom;        "Reference sequence chromosome"
+    uint   chromStart;   "Start position in chromosome"
+    uint   chromEnd;     "End position in chromosome"
+    string name;         "Human allele / Denisova ancestral allele"
+    string feature;      "Ensembl Transcript ID or Regulatory Region ID<BR>or ID of TFB profile from JASPAR or TRANSFAC"
+    string gene;         "Ensembl Gene ID"
+    string extra;        "Extra info: for coding genes, Ensembl Protein ID and/or HGNC;<BR> for Regulatory Motifs, scores & matrix ID"
+    string consequence;  "Variant Effect Predictor (VEP) consequence term"
+    string cdnaPosition; "Offset in transcript, if applicable"
+    string cdsPosition;  "Offset in coding sequence (CDS), if applicable"
+    string protPosition; "Offset in protein sequence, if applicable"
+    string aminoAcids;   "Amino acid change, if applicable"
+    string codons;       "Codon change, if applicable"
+    string humanAl;      "Modern human fixed (or major) allele on positive strand"
+    string denAl;        "Denisova (ancestral) allele"
+    string chimpAl;      "Chimpanzee ancestral allele"
+    string gorAl;        "Gorilla ancestral allele"
+    string orangAl;      "Orangutan ancestral allele"
+    string denZyg;       "Denisova zygosity of ancestral allele (homozygous/heterozygous)"
+    string dbSNP;        "dbSNP rs ID, if available"
+    float tgpFreq;       "1000 Genomes Project frequency of modern human allele"
+    string flag;         "Flag(s): CpG if in CpG island; RM if in repeat masked region;<BR> LowQual if conflicting GATK calls; SysErr if prone to systematic errors"
+    char geneStrand;     "Gene strand: '+' or '-', if applicable; otherwise '.'"
+    )