dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
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Method Detail
Submitter Method Handle: BCM-HGSC
Submitter Method ID: JWB_SNP_DISCOVERY
Submitted method description:
Reads were mapped to the reference human genome build 36
(hg18) using BLAT. Reads were realigned by cross_match to a local 40
kb fragment of the reference genome, and all variation from each
read was saved. Variant positions were aggregated by genome
coordinate and filtered to remove false positives based on the
following criteria: Variant quality score, fraction of bases at each
position that were variant and proximity to a homopolymer run of 5 bp
or longer. See wheeler et al. Nature 2008 for details.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
BCMHGSC_JDW Assay JWB_snps_no_apoe 129