| Title | Description |
| HowToInstall | How to Install the Variation toolkit |
| NgsProject | CGI interface to Samtools tview. Visualize short reads alignments |
| Vcf2Sqlite | Inserts a VCF in a sqlite3 database |
| Vcf2xml | Transforms a VCF to xml |
| FastaSlice | Slice a FASTA input |
| Scanvcf | reads some VCFs, appends a column with the sample name |
| ExtractInfo | Extract a field from the INFO column of a VCF file |
| ExtractFormat | Extract a field from the FORMAT column of a VCF file. |
| NcbiEFetch | Fetch a record from the NCBI database |
| SamplesPerSnp | Appends a column with the number of Samples per Variation |
| GroupBySnp | Creates a pivot table with the data(samples)=f(SNP) |
| NumericSplit | A simple numeric splitter |
| GroupByGene | transposes a VCF table with a 'GENE' and a 'SAMPLE' column and ouput a new table: count(Gene)=f(SAMPLE) |
| NormalizeChrom | Normalizes the name of a chromosome to/from UCSC/ENSEMBL |
| DnaContext | Prints the DNA context of a variation using a genome indexed with samtools faidx and its GC percent |
| Prediction | basic variation predictor |
| Manhattan | draws a manhattan plot as a postscript file |
| NcbiESearch | Search NCBI/Entrez |
| VcfTTView | Prints the BAM alignments around variations. |
| VCFTabix | Intersection VCF/Tabix |
| MysqlQuery | Sends a mysql query for each row |
| MysqlUcsc | Intersection VCF/UCSC mysql data. |
| VcfBigWig | Intersection VCF/BigWig |
| VcfBigBed | Intersection VCF/BigBed |
| Verticalize | Verticalize a table |
| UniProt | Take as input a position on a protein and an uniprot ACN, connect to uniprot.org and answers wether a amino acid is contained in a 'feature' |
| PfamScan | Take as input a position on a protein and an uniprot ACN, connect to pfam.sanger.ac.uk and answers wether a amino acid is contained in a 'match'. |
| Vcf2bed | Generates a BED file from a VCF |
| EmblStringSesolve | Calls the service: EMBL String resolve |
| EmblStringInteractors | Calls the service: EMBL String interactors |
| EmblStringInteractions | Calls the service: EMBL String interactions |
| VcfCut | (very) simple 'cut this region' |
| UcscGenesPs | Visualization of the mutations in the UCSC genes |
| VcfIntersect | Compute the intersection for an ordered VCF/BED with another source |
| Bam2wig | Creates a WIG file for the coverage of a BAM file |
| Ttmap | prints an ASCII genomic map |
| VcfLiftOver | Use the UCSC C API to process the data with 'liftOver' |
| BackLocate | convert a protein variation to a genomic position |
| GenomeSim | Generates two mutated homologous sequences from a fasta file |
| FastaSortUniq | sort/uniq on FASTA sequences |
| FastaRevComp | reverse complement FASTA sequences |
| FastaTail | Prints the last sequences of a list of FASTA sequences |
| Fasta2Term | colorizes some fasta sequences when printing to stdout. |
| Fasta2Tsv | prints Fasta Sequences as Tab delimited values |
| FastaTac | Reverse the order of some fasta sequences |
| NcbiELink | Retrieves related NCBI records using NCBI-ELink |
| NcbiCited | Retrieves NCBI/Pubmed records citing a pmid using NCBI-ELink |
| Protein2Genome | Maps a protein start/end back to the genome |
| XsltStream | applies a XSLT stylesheet to some fragments of a SAX/XML stream. |
| GeneOntologyDbManager | Utilities for Gene Ontology |
| ShowProgress | Displays a progress bar on the console |
| Casava2Vcf | Transforms Casava SNPs and INDEL to VCF |
| VcfId | fills the ID columns of a VCF using UCSC/snpX |
| VcfEvs | Annotates a VCF with the data from exome variant server |
| VcfNumericFilter | Filters a VCF-like file on a numeric value |
| TeeC | Tee for counting the rows |