b73f216db33fc474f4ec57ec8638fef390d69cef jnavarr5 Tue Nov 5 13:16:41 2024 -0800 Making changes from the code review, refs #34767 diff --git src/hg/makeDb/trackDb/human/dbSnp155Composite.html src/hg/makeDb/trackDb/human/dbSnp155Composite.html index bca4d8b..a622dfe 100644 --- src/hg/makeDb/trackDb/human/dbSnp155Composite.html +++ src/hg/makeDb/trackDb/human/dbSnp155Composite.html @@ -610,31 +610,32 @@
  • bigBedToBed converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options.
  • bigBedNamedItems extracts rows for one or more rs# IDs.
  • Example: retrieve all variants in the region chr1:200001-200400

    bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout

    Example: retrieve variant rs6657048

    bigBedNamedItems dbSnp155.bb rs6657048 stdout
    -

    Example: retrieve all variants with rs# IDs in file myIds.txt

    +

    Example: retrieve all variants with rs# IDs in a file (myIds.txt) + and output to another file (dbSnp155.myIds.bed)

    bigBedNamedItems -nameFile dbSnp155.bb myIds.txt dbSnp155.myIds.bed

    The columns in the bigDbSnp/bigBed files and dbSnp155Details.tab.gz file are described in bigDbSnp.as and dbSnpDetails.as respectively. For columns that contain lists of allele frequency data, the order of projects providing the data listed is as follows:

    1. 1000Genomes