| samtools flags |
samtools flags INT|STR[,...] |
Convert between textual and numeric flag representation. |
| faRandomize |
faRandomize [-seed=N] in.fa randomized.fa |
Program to create random fasta records |
| ixIxx |
ixIxx in.text out.ix out.ixx |
Create indices for simple line-oriented file of format<symbol> <free text> |
| pslToBed |
pslToBed psl bed |
pslToBed: tranform a psl format file to a bed format file. |
| raToTab |
raToTab in.ra out.tab |
Convert ra file to table. |
| gmtime |
gmtime |
Convert unix timestamp to date string |
| autoXml |
autoXml file.dtdx root |
Generate structures code and parser for XML file from DTD-like spec |
| bigBedInfo |
bigBedInfo file.bb |
Show information about a bigBed file. |
| netSplit |
netSplit in.net outDir |
Split a genome net file into chromosome net files |
| bedGeneParts |
bedGeneParts part in.bed out.bed |
Given a bed, spit out promoter, first exon, or all introns. |
| hgGcPercent |
hgGcPercent [options] database nibDir |
Calculate GC Percentage in 20kb windows |
| paraFetch |
paraFetch N R URL {outPath} |
Try to fetch url with multiple connections |
| genePredCheck |
genePredCheck [options] fileTbl .. |
Validate genePred files or tables |
| rmFaDups |
rmFaDup oldName.fa newName.fa |
Remove duplicate records in FA file |
| sizeof |
sizeof |
Show size of various C types for reference |
| textHistogram |
textHistogram [options] inFile |
Make a histogram in ascii |
| samtools dict |
samtools dict <ref.fasta|ref.fasta.gz> |
Create a sequence dictionary file from a fasta file. |
| dbTrash |
dbTrash -age=N [-drop] [-historyToo] [-db=<DB>] [-verbose=N] |
Drop tables from a database older than specified N hours |
| genePredHisto |
genePredHisto [options] what genePredFile histoOut |
Get data for generating histograms from a genePred file. |
| gff3ToPsl |
gff3ToPsl mapFile inGff3 out.psl |
Convert a GFF3 CIGAR file to a PSL file |