# HG changeset patch # User aaronquinlan # Date 1323283091 18000 # Node ID 804fbeaa8419c3b9a5bc4e04e04e4d64b1c5a8fd # Parent b9c28ef04ea9e24737ad369176761ff496bed29e Uploaded diff -r b9c28ef04ea9 -r 804fbeaa8419 bedtools-galaxy/bamToBed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedtools-galaxy/bamToBed.xml Wed Dec 07 13:38:11 2011 -0500 @@ -0,0 +1,75 @@ + + + + + bamToBed + + + + bamToBed $option $ed_score -i '$input' > '$output' + #if str($tag): + -tag $tag + #end if + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool converts a BAM file to a BED file. The end coordinate is computed +by inspecting the CIGAR string. The QNAME for the alignment is used as the +BED name field and, by default, the MAPQ is used as the BED score. + +------- + +**Options**:: + + -bedpe Write BEDPE format. + - Requires BAM to be grouped or sorted by query. + + -bed12 Write "blocked" BED format (aka "BED12"). + http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1 + + -split Report "split" BAM alignments as separate BED entries. + + -ed Use BAM edit distance (NM tag) for BED score. + * Default for BED is to use mapping quality. + * Default for BEDPE is to use the minimum of the two mapping qualities for the pair. + * When -ed is used with -bedpe, the total edit distance from the two mates is reported. + + -tag Use other NUMERIC BAM alignment tag for BED score. + * Default for BED is to use mapping quality. + * Disallowed with BEDPE output. + + +------ + + +This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__. + +.. __: http://code.google.com/p/bedtools/ +.. __: http://cphg.virginia.edu/quinlan/ + + +