# HG changeset patch # User nilesh # Date 1373483234 14400 # Node ID 5ff4702264f7427ecc010f7764a032c02d2b2777 # Parent 438b5c8d736c6f1f4d1a92ce70d3020d30ad71e5 Uploaded diff -r 438b5c8d736c -r 5ff4702264f7 tabix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tabix.xml Wed Jul 10 15:07:14 2013 -0400 @@ -0,0 +1,89 @@ + + Generic indexer for TAB-delimited genome position files. + + tabix + + + tabix + #if str($position) == "no" + -0 + #end if + + #if str($options.extension) == "tabular" + #if str($options.columnseq) != "" + -s $options.columnseq + #end if + + #if str($options.columnstart) != "" + -b $options.columnstart + #end if + + #if str($options.columnend) != "" + -e $options.columnend + #end if + + #if str($options.skiplines) != "" + -S $options.skiplines + #end if + + #if str($options.skipchar) != "" + -c $options.skipchar + #end if + #else + -p + #end if + + $input $region + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does:** + +Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. + +**Citation:** + +Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. + +http://samtools.sourceforge.net/tabix.shtml + +**Example:** + +(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; + +tabix -p gff sorted.gff.gz; + +tabix sorted.gff.gz chr1:10,000,000-20,000,000; + + +