Category
Generic
Usage
netFilter in.net(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
-minScore=N - restrict to those scoring at least N
-maxScore=N - restrict to those scoring less than N
-minGap=N - restrict to those with gap size (tSize) >= minSize
-minAli=N - restrict to those with at least given bases aligning
-maxAli=N - restrict to those with at most given bases aligning
-minSizeT=N - restrict to those at least this big on target
-minSizeQ=N - restrict to those at least this big on query
-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
-type=XXX - restrict to given type, maybe repeated to allow several types
-syn - do filtering based on synteny (tuned for human/mouse).
-minTopScore=N - Minimum score for top level alignments. default 300000
-minSynScore=N - Min syntenic block score (def=200,000).
Default covers 27,000 bases including 9,000
aligning--a very stringent requirement.
-minSynSize=N - Min syntenic block size (def=20,000). -
-minSynAli=N - Min syntenic alignment size(def=10,000). -
-maxFar=N - Max distance to allow synteny (def=200,000).
-nonsyn - do inverse filtering based on synteny (tuned for human/mouse).
-chimpSyn- do filtering based on synteny (tuned for human/chimp).
-fill - Only pass fills, not gaps. Only useful with -line.
-gap - Only pass gaps, not fills. Only useful with -line.
-line - Do this a line at a time, not recursing
-noRandom- suppress chains involving 'random' chromosomes
-noHap- suppress chains involving chromosome names inc '_hap'
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