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 @@ <li><b>bigBedToBed</b> 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.</li> <li><b>bigBedNamedItems</b> extracts rows for one or more rs# IDs.</li> </ul> </p> <h4>Example: retrieve all variants in the region chr1:200001-200400</h4> <pre><tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout</tt></pre> <h4>Example: retrieve variant rs6657048</h4> <pre><tt>bigBedNamedItems dbSnp155.bb rs6657048 stdout</tt></pre> -<h4>Example: retrieve all variants with rs# IDs in file myIds.txt</h4> +<h4>Example: retrieve all variants with rs# IDs in a file (myIds.txt) + and output to another file (dbSnp155.myIds.bed)</h4> <pre><tt>bigBedNamedItems -nameFile dbSnp155.bb myIds.txt dbSnp155.myIds.bed</tt></pre> <p> The columns in the bigDbSnp/bigBed files and dbSnp155Details.tab.gz file are described in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/lib/bigDbSnp.as" target=_blank>bigDbSnp.as</a> and <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/lib/dbSnpDetails.as" target=_blank>dbSnpDetails.as</a> respectively. For columns that contain lists of allele frequency data, the order of projects providing the data listed is as follows: <ol> <li> <a href="https://www.internationalgenome.org/" target=_blank>1000Genomes</a>