Software Usage Function
bigBedToBed bigBedToBed output.bed Convert from bigBed to ascii bed format.
gff3ToGenePred gff3ToGenePred inGff3 outGp Convert a GFF3 file to a genePred file
bedGraphToBigWig bedGraphToBigWig in.bedGraph chrom.sizes Convert a bedGraph file to bigWig format.
bigWigToBedGraph bigWigToBedGraph in.bigWig out.bedGraph Convert from bigWig to bedGraph format.
twoBitToFa twoBitToFa input.2bit output.fa Convert all or part of .2bit file to fasta
genePredToBed genePredToBed in.genePred out.bed Convert from genePred to bed format
lavToAxt lavToAxt in.lav tNibDir qNibDir out.axt Convert blastz lav file to an axt file (which includes sequence)
wiggletools wiggletools sum [bigwig files...] Merge BigWig files
bedtools bedtobam bedtools bedtobam [OPTIONS] -i <bed/gff/vcf> -g <genome> Converts feature records to BAM format (also known as bedToBam)
bedtools bed12tobed6 bedtools bed12tobed6 [OPTIONS] -i <bed12> Splits BED12 features into discrete BED6 features (also know as bed12ToBed6)