Java utilities for Next Generation Sequencing
Pierre Lindenbaum PhD
http://plindenbaum.blogspot.com
##Tools
###Main
| Tool | Description |
|---|---|
| SplitBam | Split a BAM by chromosome group. Creates EMPTY bams if no reads was found for a given group. |
| SamJS | Filtering a SAM/BAM with javascript (rhino). |
| VCFFilterJS | Filtering a VCF with javascript (rhino) |
| SortVCFOnRef | Sort a VCF using the order of the chromosomes in a REFerence index. |
| Illuminadir | Create a structured (**JSON** or **XML**) representation of a directory containing some Illumina FASTQs. |
| BamStats04 | Coverage statistics for a BED file. It uses the Cigar string instead of the start/end to compute the coverage |
| BamStats01 | Statistics about the reads in a BAM. |
| VCFBed | Annotate a VCF with the content of a BED file indexed with tabix. |
| VCFPolyX | Number of repeated REF bases around POS. |
| VCFBigWig | Annotate a VCF with the data of a bigwig file. |
| VCFTabixml | Annotate a value from a vcf+xml file.4th column of the BED indexed with TABIX is a XML string. |
###Less used, but useful
| Tool | Description |
|---|---|
| VCFPredictions | Basic variant prediction using UCSC knownGenes. |
| FindCorruptedFiles | Reads filename from stdin and prints corrupted NGS files (VCF/BAM/FASTQ). |
| VCF2XML | Transforms a VCF to XML. |
| VCFAnnoBam | Annotate a VCF with the Coverage statistics of a BAM file + BED file of capture. It uses the Cigar string instead of the start/end to get the voverage |
| VCFTrio | Check for mendelian incompatibilities in a VCF. |
| SamGrep | Search reads in a BAM |
| VCFFixIndels | Fix samtools INDELS for @SolenaLS |
| NgsFilesSummary | Scan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..). |
| NoZeroVariationVCF | creates a VCF containing one fake variation if the input is empty. |
| HowManyBamDict | for @abinouze : quickly find the number of distinct BAM Dictionaries from a set of BAM files. |
| ExtendBed | Extends a BED file by 'X' bases. |
| CmpBams | Compare two or more BAMs. |
| IlluminaFastqStats | Statistics on Illumina Fastqs |
| Bam2Raster | Save a BAM alignment as a PNG image. |
| VcfRebase | Finds restriction sites overlapping variants in a VCF file |
| FastqRevComp | Reverse complement a FATQ file for mate-pair alignment |
| PicardMetricsToXML | Convert picards metrics file to XML. |
| Bam2Wig | Bam to Wiggle converter |
###One shots, Answers to biostar,...
| Tool | Description |
|---|---|
| BlastMapAnnots | Maps uniprot/genbank annotations on a blast result. See http://www.biostars.org/p/76056 |
| VcfViewGui | Simple java-Swing-based VCF viewer. |
| Biostar81455 | Defining precisely the genomic context based on a position http://www.biostars.org/p/81455/ |
| MapUniProtFeatures | map Uniprot features on reference genome. |
| Biostar86363 | Set genotype of specific sample/genotype comb to unknown in multisample vcf file. |
| FixVCF | Fix a VCF HEADER when I forgot to declare a FILTER or an INFO field in the HEADER |
| Biostar78400 | Add the read group info to the sam file on a per lane basis |
| Biostar78285 | Extract regions of genome that have 0 coverage See http://www.biostars.org/p/78285/ |
| Biostar77288 | Low resolution sequence alignment visualization http://www.biostars.org/p/77288/ |
| Biostar77828 | Divide the human genome among X cores, taking into account gaps See http://www.biostars.org/p/77828/ |
| Biostar76892 | Fix strand of two paired reads close but on the same strand http://www.biostars.org/p/76892/ |
| VCFCompareGT | VCF : compare genotypes of two or more callers for the same samples. |
| SAM4WebLogo | Creates an Input file for BAM + WebLogo. |
| SAM2Tsv | Tabular view of each base of the reads vs the reference. |
| Biostar84786 | Table transposition |
| VCF2SQL | Generate the SQL code to insert a VCF into a database |
| Bam4DeseqIntervals | creates a table for DESEQ with the number of reads within a sliding window for multiple BAMS |
| VCFStripAnnotations | Removes one or more field from the INFO column from a VCF. |
| VCFGeneOntology | Finds the GO terms for VCF annotated with SNPEFF or VEP |
| VCFFilterGO | Set the VCF FILTERs on VCF files annotated with SNPEFF or VCP testing wether a Gene belong or not to the descendants of a GO term. |
| Biostar86480 | Genomic restriction finder See http://www.biostars.org/p/86480/ |
| BamToFastq | Shrink your FASTQ.bz2 files by 40+% using this one weird tip by ordering them by alignment to reference |
| PadEmptyFastq | Pad empty fastq sequence/qual with N/# |
| SamFixCigar | Replace 'M'(match) in SAM cigar by 'X' or '=' |