Software Usage Function
wigCorrelate wigCorrelate one.wig two.wig ... n.wig Produce a table that correlates all pairs of wigs
gtfToGenePred gtfToGenePred gtf genePred Convert a GTF file to a genePred
liftOverMerge liftOverMerge oldFile newFile Merge multiple regions in BED 5 filesgenerated by liftOver -multiple
rowsToCols rowsToCols in.txt out.txt Convert rows to columns and vice versa in a text file.
axtChain axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain Chain together axt alignments.
chainFilter chainFilter file(s) Filter chain files. Output goes to standard out.
bedToGenePred bedToGenePred bedFile genePredFile Convert bed format files to genePred format
faFilter faFilter [options] in.fa out.fa Filter fasta records, selecting ones that match the specified conditions
bigBedSummary bigBedSummary chrom start end dataPoints Extract summary information from a bigBed file.
bigWigAverageOverBed bigWigAverageOverBed in.bed Compute average score of big wig over each bed, which may have introns.
chainStitchId chainStitchId in.chain out.chain Join chain fragments with the same chain ID into a singlechain per ID. Chain fragments must be from same original chain butmust not overlap. Chain fragment scores are summed.
bedExtendRanges bedExtendRanges database length files(s) Extend length of entries in bed 6+ data to be at least the given length, taking strand directionality into account.
chainToPsl chainToPsl in.chain tSizes qSizes target.lst query.lst out.psl Convert chain file to psl format
twoBitMask twoBitMask input.2bit maskFile output.2bit Apply masking to a .2bit file, creating a new .2bit file
chainNet chainNet in.chain target.sizes query.sizes Make alignment nets out of chains
pslCDnaFilter pslCDnaFilter [options] inPsl outPsl Filter cDNA alignments in psl format
catUncomment catUncomment file(s) catUncomment - Concatenate input removing lines that start with '#'Output goes to stdout
ldHgGene ldHgGene database table file(s).gff Load database with gene predictions from a gff file.
catDir catDir dir(s) catDir - concatenate files in directory to stdout.For those times when too many files for cat to handle.
hgsqldump hgsqldump [OPTIONS] database [tables] Execute mysqldump using passwords from .hg.conf