Category
Generic
Usage
chainFilter file(s)
Manual
This tool is part of UCSC Genome Browser's utilities.
options:
-q=chr1,chr2 - restrict query side sequence to those named
-notQ=chr1,chr2 - restrict query side sequence to those not named
-t=chr1,chr2 - restrict target side sequence to those named
-notT=chr1,chr2 - restrict target side sequence to those not named
-id=N - only get one with ID number matching N
-minScore=N - restrict to those scoring at least N
-maxScore=N - restrict to those scoring less than N
-qStartMin=N - restrict to those with qStart at least N
-qStartMax=N - restrict to those with qStart less than N
-qEndMin=N - restrict to those with qEnd at least N
-qEndMax=N - restrict to those with qEnd less than N
-tStartMin=N - restrict to those with tStart at least N
-tStartMax=N - restrict to those with tStart less than N
-tEndMin=N - restrict to those with tEnd at least N
-tEndMax=N - restrict to those with tEnd less than N
-qOverlapStart=N - restrict to those where the query overlaps a region starting here
-qOverlapEnd=N - restrict to those where the query overlaps a region ending here
-tOverlapStart=N - restrict to those where the target overlaps a region starting here
-tOverlapEnd=N - restrict to those where the target overlaps a region ending here
-strand=? -restrict strand (to + or -)
-long -output in long format
-zeroGap -get rid of gaps of length zero
-minGapless=N - pass those with minimum gapless block of at least N
-qMinGap=N - pass those with minimum gap size of at least N
-tMinGap=N - pass those with minimum gap size of at least N
-qMaxGap=N - pass those with maximum gap size no larger than N
-tMaxGap=N - pass those with maximum gap size no larger than N
-qMinSize=N - minimum size of spanned query region
-qMaxSize=N - maximum size of spanned query region
-tMinSize=N - minimum size of spanned target region
-tMaxSize=N - maximum size of spanned target region
-noRandom- suppress chains involving '_random' chromosomes
-noHap- suppress chains involving '_hap' chromosomes
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