50d9453206becf6203aa41b831cca95ba6b5b58d max Thu Sep 22 10:31:16 2022 -0700 adding decode and 1k Genomes genetic maps, refs #30044 diff --git src/hg/makeDb/autoSql/recombEvents.as src/hg/makeDb/autoSql/recombEvents.as new file mode 100644 index 0000000..71f2dde --- /dev/null +++ src/hg/makeDb/autoSql/recombEvents.as @@ -0,0 +1,30 @@ +# # Chr (chromosome) +# lbnd (lower edge of crossover event in GRCh38 coordinates) +# ubnd (upper edge of crossover event in GRCh38 coordinates) +# pid (proband ID) +# ptype (parent type as P:paternal or M:maternal) +# medsnp (physical position of median location of crossover in GRCh38 coordinates) +# complex (indicates if crossover is complex; 1:complex, 0:non-complex, NA:not tested) +# Chr lbnd ubnd pid ptype medsnp complex + +table recombEvents +"Browser extensible data (12 fields) plus two sequences" + ( + string chrom; "Chromosome (or contig, scaffold, etc.)" + uint chromStart; "Start position in chromosome" + uint chromEnd; "End position in chromosome" + string name; "Name of item" + #uint score; "Score from 0-1000" + #char[1] strand; "+ or -" + #uint thickStart; "Start of where display should be thick (start codon)" + #uint thickEnd; "End of where display should be thick (stop codon)" + #uint reserved; "Used as itemRgb as of 2004-11-22" + #int blockCount; "Number of blocks" + #int[blockCount] blockSizes; "Comma separated list of block sizes" + #int[blockCount] chromStarts; "Start positions relative to chromStart" + #string seq1; "sequence 1, normally left paired end" + #string seq2; "sequence 2, normally right paired end" + string ptype; "Parent Type (P=Paternal, M=Maternal)" + string medsnp; "Position of median location of crossover" + string complex; "1:complex, 0:non-complex, NA:not tested" + )