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The current Batch GVS version is 4.00, May 9, 2008.
A new database with dbSNP build 128 is in place.
Previous Build Notes
With the May 5, 2008 build, it is now possible to do chromosome one-base queries with chr*:base.
fastPHASE calculations were made available in the March 28, 2008 build.
For the December 24, 2007 build, the annotation parameter, if present, is recognized for displayType snpSummary, as well as tagSNPs and r2LD.
Three new annotation columns have been added to display the raw number of alleles in the set: NumberAlleles, NumberMajorAlleles, NumberMinorAlleles.
There has been a change in the assignment of the minor allele for the rare triallele case: the minor allele is no longer the least frequent
allele, but the second most frequent allele (that is the more frequent of the two minor alleles).
For the December 14, 2007 build, there is a new parameter returnTarballWithEmailMessage for downloading a tarball that includes the email message.
For the December 6, 2007 build, the chimp allele has been added for snpSummary data; this puts an extra column in the middle of the output.
For the December 5, 2007 build, the per-file limits for large tagSNPs jobs has been reduced from 100,000 to
60,000 without multipop and 30,000 with multipop.
For the October 16, 2007 build, copy number variations have been added to the SNP annotation list. A bug was fixed: previously, when
tag SNPs were requested, and the frequency cutoff was not specified, no results were returned; now the frequency cutoff will
default to 0 when not specified, and there will be a result file. There is a new searchType: chipID.
In the September 27, 2007 build, CopyNumberVariation has been added to the annotation list. There is now an additional
copy-number column in the SNP summary output, just before the flank columns.
As of the September 11, 2007 build, the chipFilter parameter can be used for the snpSummary displayType.
For the August 7, 2007 build, the speed and memory footprint for the r2LD display has been improved. This does not affect the usage.
Also added was the Illumina HumanHap300 version 2 chip.
Note prior to August 7, 2007 : There is a new noMonomorphic parameter. The default is "true", so that monomorphic (single-allele) SNPs will be
excluded unless this parameter is set to false. The SNP positions now include the chromosome number separated from the
base by a colon. The freqCutoff parameter is now used by all display types. The frequency and monomorphic
filtering has been changed to match the recently-improved handling on the GVS site (filters applied after the genotypes
have been sorted into population groups). As a result, the multipop
parameter now has a default value of true, and multiple populations can be submitted with this parameter either true or false.
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National Heart, Lung, and Blood Institute
Programs for Genomic Applications