37bccf08f043153ebad2bc6bfe4f5860a298ee9c max Mon Mar 9 03:09:49 2015 -0700 typo in help message diff --git src/hg/hgBeacon/help.txt src/hg/hgBeacon/help.txt index f62b782..cda3143 100644 --- src/hg/hgBeacon/help.txt +++ src/hg/hgBeacon/help.txt @@ -1,25 +1,25 @@
A Genomics Alliance Beacon at UCSC, see http://ga4gh.org/#/beacon In collaboration with the Leiden Open Variation Database and Biobase/HGMD. parameters: - chromosome: 1 - 22, X, Y or M - position: 0-based position on chromosome - dataset: either "lovd" or "hgmd". If not provided, queries both LOVD and HGMD. -"- reference: optional. if specified, has to be "GRCh37" +- reference: optional. if specified, has to be "GRCh37" - alternateBases: A,C,T or G. Ignored for HGMD (HGMD gives out only positions, not the alleles, these are only on their website) - format: if "text", does not return JSON, but just one of the words "true", "false" or "overlap". Easier to parse for simple shell scripts. For alleles with a "true" reply, you can get more details about a variant from the source databases: - dataset lovd: Use the LOVD API to get all info, see chapter 9 of the LOVD manual, http://www.lovd.nl/3.0/docs/LOVD_manual_3.0.pdf Or search manually on http://www.lovd.nl/3.0/home - dataset hgmd: Create an account on http://www.hgmd.cf.ac.uk/ and search manually for the variant. Note that only single-basepair substitutions are available from both databases. Insertions and deletions might be available with later versions of the Beacon