| samjs | Filters a BAM using a javascript expression ( java nashorn engine ). | sam bam nashorn javascript filter | | |
|---|
| casectrljfx | chart of case/control maf from a VCF and a pedigree | vcf pedigree case control visualization jfx chart maf | | |
|---|
| pubmedcodinglang | Programming language use distribution from recent programs / articles | pubmed xml code programming | | |
|---|
| vcffixindels | Fix samtools indels (for @SolenaLS) | vcf indel | | use `bcftools norm`. |
|---|
| vcftail | print the last variants of a vcf | vcf | | |
|---|
| vcfhead | print the first variants of a vcf | vcf | | |
|---|
| vcfmulti2oneallele | 'one variant with N ALT alleles' to 'N variants with one ALT' | vcf | | |
|---|
| vcfin | Only prints variants that are contained/not contained into another VCF | vcf compare | | |
|---|
| vcfpredictions | Basic Variant Effect prediction using gtf | vcf annotation prediction gtf | | |
|---|
| vcffilterso | Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology. Reasoning : Children of user's SO-terms will be also used. | vcf filter sequenceontology prediction so | | |
|---|
| vcffilterjs | Filtering VCF with javascript expressions | vcf filter javascript json nashorn | | |
|---|
| vcfpolyx | Number of repeated REF bases around POS. | vcf repeat | | |
|---|
| vcfbed | Transfer information from a BED to a VCF | bed vcf annotation | | |
|---|
| vcftrio | Find mendelian incompatibilitie / denovo variants in a VCF | vcf mendelian pedigree denovo | | |
|---|
| groupbygene | Group VCF data by gene/transcript. By default it uses data from VEP , SnpEff | vcf gene | | |
|---|
| addlinearindextobed | Use a Sequence dictionary to create a linear index for a BED file. Can be used as a X-Axis for a chart. | bed reference | | |
|---|
| almostsortedvcf | Sort an 'almost' sorted VCF. Most variants should be sorted but a few consecutive lines might have been switched by a caller. | | | |
|---|
| backlocate | Mapping a mutation on a protein back to the genome. | vcf annotation prediction protein | | |
|---|
| bam2fastq | convert paired-end SAM to fastq using a memory buffer. | fastq bam | | |
|---|
| bam2raster | BAM to raster graphics | bam alignment graphics visualization png | | |
|---|
| bam2svg | BAM to Scalar Vector Graphics (SVG) | bam alignment graphics visualization svg | | |
|---|
| bam2xml | converts a BAM to XML | sam bam xml | | |
|---|
| bam2wig | Bam to fixedStep Wiggle converter , or BED GRAPH. Parses the cigar String to get the depth. Memory intensive: must alloc sizeof(int)*size(chrom) | bam wig wiggle bed | | |
|---|
| bamcmpcoverage | Creates the figure of a comparative view of the depths sample vs sample. Memory consideration: the tool alloc an array of bits which size is: (MIN(maxdepth-mindepth,pixel_width_for_one_sample) * count_samples)^2 | sam bam visualization coverage | | |
|---|
| bamrenamechr | Convert the names of the chromosomes in a BAM file | sam bam chromosome contig | | |
|---|
| bamstats04 | Coverage statistics for a BED file. | sam bam coverage depth statistics bed | | |
|---|
| bamstats05 | Coverage statistics for a BED file, group by gene | bam coverage statistics bed | | |
|---|
| batchigvpictures | Takes IGV pictures in batch. Save as HTML+png image | gui igv visualization | | |
|---|
| bedliftover | Lift-over a VCF file | bed liftover | | |
|---|
| bedrenamechr | Convert the names of the chromosomes in a Bed file | bed chromosome contig convert | | |
|---|
| biostar103303 | Calculate Percent Spliced In (PSI). | sam bam psi | | |
|---|
| biostar130456 | Split individual VCF files from multisamples VCF file | vcf samples sample | | |
|---|
| biostar59647 | SAM/BAM to XML | sam bam xml | | |
|---|
| biostar76892 | fix strand of two paired reads close but on the same strand. | sam bam | | |
|---|
| biostar77288 | Low resolution sequence alignment visualization | bam sam visualization svg alignment | | |
|---|
| biostar77828 | Divide the human genome among X cores, taking into account gaps | workflow reference parallel | | |
|---|
| biostar78285 | Extract BAMs coverage as a VCF file. | sam bam depth coverage | | |
|---|
| biostar78400 | add the read group info to the sam file on a per lane basis | sam bam xml read-group | | |
|---|
| biostar81455 | Defining precisely the exonic genomic context based on a position . | bed gene gtf | | |
|---|
| biostar84452 | remove clipped bases from a BAM file | sam bam clip | | |
|---|
| biostar84786 | Matrix transposition | matrix util | | |
|---|
| biostar86363 | Set genotype of specific sample/genotype comb to unknown in multisample vcf file. See http://www.biostars.org/p/86363/ | sample genotype vcf | | |
|---|
| biostar86480 | Genomic restriction finder | rebase genome enzyme restricion genome fasta | | |
|---|
| biostar90204 | Bam version of linux split. | sam bam split util | | |
|---|
| msa2vcf | Getting a VCF file from a CLUSTAW or a FASTA alignment. | vcf snp msa alignment | | use https://github.com/sanger-pathogens/snp_sites. |
|---|
| biostar95652 | Drawing a schematic genomic context tree. | genbank svg tree evolution | | |
|---|
| biostar139647 | Convert alignment in Fasta/Clustal format to SAM/BAM file | msa sam bam clustal | | |
|---|
| biostar145820 | subsample/shuffle BAM to fixed number of alignments. | sam bam shuffle | | |
|---|
| blastmapannots | Maps uniprot/genbank annotations on a blast result. | blast annotation genbank uniprot | | |
|---|
| buildwpontology | Build a simple RDFS/XML ontology from the Wikipedia Categories | wikipedia ontology rdf gui | | |
|---|
| bwamemdigest | | | | |
|---|
| bwamemnop | Merge the other BWA-MEM alignements with its SA:Z:* attributes to an alignment containing a cigar string with 'N' ( Skipped region from the reference.) | bwa sam bam | | |
|---|
| cmpbams | Compare two or more BAM files | sam bam compare | | |
|---|
| cmpbamsandbuild | Compare two BAM files mapped on two different builds. Requires a liftover chain file | | | |
|---|
| coveragenormalizer | normalize BAM coverage | | | |
|---|
| downsamplevcf | DownSample a VCF. Will keep 'n' random variants in a vcf. | vcf | | |
|---|
| evs2vcf | Download data from EVS http://evs.gs.washington.edu/EVS as a BED chrom/start/end/XML For later use, see VCFTabixml. | | | |
|---|
| evsdumpxml | Download data from EVS http://evs.gs.washington.edu/EVS as XML file. | | | |
|---|
| fastq2fasta | fastq -> fasta | fastq fasta | | use awk, samtools.... |
|---|
| kg2bed | converts UCSC knownGenes file to BED. | ucsc bed knownGenes | | |
|---|
| fastqentropy | Compute the Entropy of a Fastq file (distribution of the length(gzipped(sequence)) | fastq | | |
|---|
| fastqgrep | Grep reads names in fastq | fastq | | use picard. |
|---|
| fastqjs | Filters a FASTQ file using javascript( java nashorn engine). | fastq | | |
|---|
| fastqphred64to33 | Convert Illumina Fastq 64 encoding to Fastq 33 | fastq | | |
|---|
| fastqrevcomp | produces a reverse-complement fastq (for mate pair alignment see http://seqanswers.com/forums/showthread.php?t=5085 ) | fastq | | |
|---|
| fastqshuffle | Shuffle Fastq files | fastq | | |
|---|
| fastqsplitinterleaved | Split interleaved Fastq files. | fastq | | |
|---|
| findallcoverageatposition | Find depth at specific position in a list of BAM files. My colleague Estelle asked: in all the BAM we sequenced, can you give me the depth at a given position ? | bam coverage search depth | | |
|---|
| findavariation | Finds a specific mutation in a list of VCF files | vcf variation search find bcf | | |
|---|
| findcorruptedfiles | Reads filename from stdin and prints corrupted NGS files (VCF/BAM/FASTQ/BED/TBI/BAI) | vcf bam fastq bed | | |
|---|
| findmyvirus | Find my Virus. Created for Adrien Inserm. Proportion of reads mapped on HOST/VIRUS. | bam virus | | |
|---|
| findnewsplicesites | use the 'N' operator in the cigar string to find unknown splice sites | bam sam rnaseq splice gtf | | |
|---|
| fixvcf | Fix a VCF if INFO or FILTER are missing | | | |
|---|
| fixvcfformat | Fix PL format in VCF. Problem is described in http://gatkforums.broadinstitute.org/discussion/3453 | | | |
|---|
| fixvcfmissinggenotypes | After a VCF-merge, read a VCF, look back at some BAMS to tells if the missing genotypes were homozygotes-ref or not-called. If the number of reads is greater than min.depth, then a missing genotype is said hom-ref. | sam bam vcf sv genotype | | |
|---|
| gcpercentanddepth | Extracts GC% and depth for multiple bam using a sliding window | gc% depth coverage | | |
|---|
| genomicjaspar | Find jaspar patterns in FASTA sequences. Reports a BED file. | jaspar genomic pattern | | |
|---|
| howmanybamdict | finds if there's are some differences in the sequence dictionaries. | sam bam dict vcf | | |
|---|
| illuminadir | Create a structured (**JSON** or **XML**) representation of a directory containing some Illumina FASTQs. | json xml illumina fastq workflow | | |
|---|
| ilmnfastqstats | Reads filenames from stdin: Count FASTQs in Illumina Result. | | | |
|---|
| impactofduplicates | Impact of Duplicates per BAM. | bam | | |
|---|
| liftover2svg | Convert LiftOver chain files to animated SVG | svg liftover ucsc xml | | |
|---|
| mapuniprot | map uniprot features on reference genome | uniprot bed fasta reference xml | | |
|---|
| mergesplittedblast | merge blast Hits from splitted BLAST database | blast | | |
|---|
| ncbitaxonomy2xml | Dump NCBI taxonomy tree as a hierarchical XML document | taxonomy ncbi xml | | |
|---|
| samjmx | Monitor/interrupt/break a BAM/SAM stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.html | sam bam jmx monitoring | | |
|---|
| ngsfilessummary | Scan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..). Useful to get a summary of your samples. | sam bam vcf util | | |
|---|
| noemptyvcf | If VCF is empty or doesn't exists, create a dummy one | | | Was developped at the time where VEP didn't send an output if there was no variant, just a header in the source vcf.. |
|---|
| nozerovariationvcf | cat a whole VCF, or, if there is no variant, creates a fake one | vcf | | |
|---|
| pademptyfastq | Pad empty fastq sequence/qual with N/# | fastq | | use awk. |
|---|
| pubmeddump | Dump XML results from pubmed/Eutils | ncbi pubmed xml | | |
|---|
| pubmedorcidgraph | Creates a graph from Pubmed and Authors' Orcid identifiers | pubmed ncbi orcid | | |
|---|
| pubmedfilterjs | Filters Pubmed XML with a javascript (java rhino) expression. Context contain 'article' a PubmedBookArticle or a PubmedArticle and 'index', the index in the XML file. | pubmed javascript xml ncbi | | |
|---|
| referencetovcf | Creates a VCF containing all the possible substitutions from a Reference Genome. | vcf reference fasta | | |
|---|
| sam2json | Convert a SAM input to JSON | sam bam json | | |
|---|
| sam2psl | Convert SAM/BAM to PSL http://genome.ucsc.edu/FAQ/FAQformat.html#format2 or BED12 | sam bam psl | | use bedtools/bamtobed. |
|---|
| sam2tsv | Prints the SAM alignments as a TAB delimited file. | sam bam table cram tsv | | |
|---|
| sam4weblogo | Sequence logo for different alleles or generated from SAM/BAM | sam bam visualization logo | | |
|---|
| Samclipindelfraction | Extract clipping/indel fraction from BAM | sam bam clip | | This tool can be replace with Bioalcidaejdk. |
|---|
| samfixcigar | Fix Cigar String in SAM replacing 'M' by 'X' or '=' | sam bam cigar | | |
|---|
| samgrep | grep read-names in a bam file | sam bam | | |
|---|
| samshortinvert | Scan short inversions in SAM using supplementary reads. | sam bam sv inversion | | |
|---|
| samstats01 | Statistics about the reads in a BAM. | sam bam | | |
|---|
| sortvcfoninfo | Sort a VCF a field in the INFO column | vcf sort annotation | | |
|---|
| sortvcfonref2 | Sort a VCF using the internal dictionary or an external reference order (Deprecated: use bcftools sort). | vcf sort | | use picard sortvcf. |
|---|
| splitbytile | Split Bam By tile | sam bam | | |
|---|
| vcf2hilbert | Plot a Hilbert Curve from a VCF file. | vcf image visualization | | |
|---|
| vcf2postscript | Print VCF context as Postscript | vcf postscript | | |
|---|
| vcf2rdf | convert VCF to RDF (N3 notation) | vcf rdf | | |
|---|
| vcf2sql | Generate the SQL code to insert a VCF into mysql | vcf sql | | |
|---|
| vcf2xml | Convert VCF to XML | vcf xml | | |
|---|
| vcfbiomart | BiomartQueries with VCF | vcf ensembl biomart annotation | | |
|---|
| vcfcadd | Annotate VCF with Combined Annotation Dependent Depletion (CADD) (Kircher & al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2892.PubMed PMID: 24487276. | vcf prediction cadd annotation | | |
|---|
| vcfcmppred | Compare predictions (SNPEff, VEP) for several VCFs | | | |
|---|
| vcfcomm | Equivalent of linux comm for VCF | | | |
|---|
| vcfcompare | Compares two VCF files | vcf compare | | |
|---|
| vcfcomparegt | compare two or more genotype-callers for the same individuals. Produce a VCF with FORMAT fields indicating if a genotype is new or modified. | vcf compare | | |
|---|
| vcfconcat | Concatenante sorted VCF with same sample, does NOT merge genotypes | vcf | | |
|---|
| vcfcutsamples | Select/Exclude some samples from a VCF | vcf sample | | use bcftools or gatk SelectVariants. |
|---|
| vcfjaspar | Finds JASPAR profiles in VCF | vcf matrix jaspar | | |
|---|
| vcfliftover | Lift-over a VCF file | vcf liftover | | |
|---|
| vcfmerge | Merge a large number of VCF Files | vcf sort merge | | |
|---|
| vcfmulti2one | Convert VCF with multiple samples to a VCF with one SAMPLE, duplicating variant and adding the sample name in the INFO column | vcf sample | | |
|---|
| vcfregulomedb | Annotate a VCF with the Regulome data (http://regulome.stanford.edu/ | | | |
|---|
| vcfrenamechr | Convert the names of the chromosomes in a VCF file | vcf contig chromosome convert | | use `bcftools annotate` with `--rename-chrs file`. |
|---|
| vcfrenamesamples | Rename the Samples in a VCF | vcf sample | | |
|---|
| vcfresetvcf | Reset Genotypes in VCF (./.) if they've been found in another VCF indexed with tabix | vcf genotype | | |
|---|
| vcfsetdict | Set the `##contig` lines in a VCF header on the fly | vcf dict fai | | |
|---|
| vcfshuffle | Shuffle a VCF | vcf | | |
|---|
| vcfSimulator | Generate a VCF | vcf | | |
|---|
| vcfstats | Produce VCF statitics | vcf stats R | | |
|---|
| vcfcombinetwosnvs | Detect Mutations than are the consequences of two distinct variants. This kind of variant might be ignored/skipped from classical variant consequence predictor. Idea from @SolenaLS and then @AntoineRimbert | vcf annotation prediction protein mnv | | |
|---|
| vcfstripannot | Removes one or more field from the INFO/FORMAT column of a VCF. | vcf | | Use bcftools annotate -x . |
|---|
| vcftabixml | annotate a value from a vcf+xml file | vcf xml | | |
|---|
| vcfvcf | Get the INFO from a VCF and use it for another VCF | | | obsolete. use GATK. |
|---|
| worldmapgenome | Genome/Map of the world. Input is a BED file: chrom/start/end/country. | gis | | |
|---|
| uniprotfilterjs | Filters Uniprot DUMP+ XML with a javascript (java rhino) expression. Context contain 'entry' an uniprot entry and 'index', the index in the XML file. | unitprot javascript xjc xml | | |
|---|
| skipxmlelements | Filter XML elements with a javascript (java rhino) expression. Context contain 'element' the current element. It implementsthe interface Tag described in SkipXmlElements.class | xml javascript | | |
|---|
| vcfensemblvep | Annotate a VCF with ensembl REST API | vcf annotation rest ensembl xml xslt xsl | | |
|---|
| vcfgroupbypop | Group VCF data by population, creates a VCF where each 'SAMPLE' is a population | vcf pedigree population | | |
|---|
| bamtile | Answer to @sjackman : Is there a bedtools command to determine a minimal tiling path? A minimal set of features that cover a maximum of the target. | bam sam | | |
|---|
| xcontaminations | For @AdrienLeger2 : cross contamination between samples by looking at the homozygous genotypes. | sam bam vcf contamination | | |
|---|
| biostar3654 | show blast alignment with annotations | blast xml annotation | | |
|---|
| vcfburden | Solena: vcf to (chrom/pos/ref/alt/individus(G:0/1/2/-9) | | | deprecated. |
|---|
| vcfreplacetag | Replace the key for INFO/FORMAT/FILTER | vcf | | use `bcftools annotate` with option `-c`. |
|---|
| vcfpeekvcf | Get the INFO from a VCF and use it for another VCF | vcf annotation | | |
|---|
| vcfgetvariantbyIndex | Access a Plain or BGZF-compressed VCF file by index | vcf | | |
|---|
| vcfmulti2oneinfo | 'one INFO with N values' to 'N variants with one INFO' | vcf | | |
|---|
| bedindextabix | Index and sort a Bed on the fly with Tabix. | bed tabix | | |
|---|
| vcf2bam | vcf to bam | ref vcf bam | | |
|---|
| vcffilterxpath | Filter a VCF with a XPATH expression on a INFO tag containing a base64 encodede xml document | vcf xml xpath | | |
|---|
| biostar140111 | How to obtain human genotype data from dpSNP ftp? | | | |
|---|
| extendrefwithreads | Extending ends of sequences with the help of reads | read fastq reference sam bam | | |
|---|
| pcrslicereads | Mark PCR reads to their PCR amplicon | pcr sam bam cigar | | |
|---|
| vcfjmx | Monitor/interrupt/break a VCF stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.html | java jmx vcf | | |
|---|
| gtf2xml | Convert GTF/GFF to XML | xml gtf gff gff3 | | |
|---|
| sortsamrefname | Sort a BAM on chromosome/contig and then on read/querty name | sam sort | | |
|---|
| biostar154220 | Cap BAM to a given coverage | bam sam coverage depth | | |
|---|
| biostar160470 | Getting untranslated nucleotide sequences on tblastn standalone | blasn blast translation protein | | |
|---|
| biostar165777 | Split a XML file | xml | | |
|---|
| vcfcomparecallers | Compare two VCFs and print common/exclusive information for each sample/genotype | vcf compare genotype | | |
|---|
| bamclip2insertion | Convert SOFT clip to Insertion of other read confirm it | sam bam clip | | |
|---|
| biostar170742 | convert sam format to axt Format | sam axt | | |
|---|
| biostar172515 | Convert BAI to XML | bai bam xml | | |
|---|
| biostar173114 | make a bam file smaller by removing unwanted information see also https://www.biostars.org/p/173114/ | sam bam | | |
|---|
| biostar175929 | Construct a combination set of fasta sequences from a vcf | fasta vcf | | |
|---|
| vcfcalledwithanothermethod | Compare one vcf with other , add a flag to tell if a variant was called with another method. Vcf must be sorted on the same Dict. | vcf compare concordance | | |
|---|
| biostar178713 | split bed file into several bed files where each region is separated of any other by N bases | bed | | |
|---|
| vcfremovegenotypejs | Reset Genotype in VCF using a javascript expression | | | |
|---|
| bamstats02 | Statistics about the flags and reads in a BAM | sam bam | | |
|---|
| bamstats02view | Statistics about the flags and reads in a BAM. Visualize date from BamStats02 | | | |
|---|
| biostar105754 | bigwig : peak distance from specific genomic region | wig bigwig | | |
|---|
| bam2sql | Convert a SAM/BAM to sqlite statements | bam sam sql sqlite | | |
|---|
| vcf2zip | Reads a stream of concatenated VCFs and insert them into a Zip file | | | |
|---|
| pubmedgender | Add gender-related attributes in the Author tag of pubmed xml. | pubmed gender ncbi xml | | |
|---|
| pubmedmap | Use Pubmed Author's Affiliation to map the authors in the world. | pubmed xml gis map | | |
|---|
| splitvcf | split a vcf using a named list of intervals... | vcf | | |
|---|
| forkvcf | Fork a VCF. | | | |
|---|
| bim2vcf | convert a .bim to a .vcf . For @FlorianeS44 | bim vcf | | |
|---|
| concatsam | concat sam files | sam bam | | |
|---|
| samreadlengthdistribution | Sam read/insert length distribution | sam bam histogram | | |
|---|
| biostar214299 | Extract allele specific reads from bamfiles | sam bam variant snp | | |
|---|
| cmpbams4 | Compare two BAM files. Print a tab-delimited report | sam bam compare | | |
|---|
| biostar234081 | convert extended CIGAR to regular CIGAR ('X','=' -> 'M') | sam bam cigar | | |
|---|
| vcfgnomad | Peek annotations from gnomad | vcf annotation gnomad | | |
|---|
| vcf2svg | write a vcf to svg , with gene context | vcf svg xlm visualization | | |
|---|
| mergeblastxml | merge XML blast results (same Iteration/Iteration_query-def in multiple xml files | blast xml | | |
|---|
| vcfannotwithbeacon | Annotate a VCF with ga4gh beacon | ga4gh beacon vcf annotation | | |
|---|
| commbams | Equivalent of unix 'comm' for bams sorted on queryname | sam bam comm compare | | |
|---|
| samscansplitreads | scan split reads | sam sv splitreads clip | | |
|---|
| samretrieveseqandqual | I have a query-sorted BAM file without read/qual sequences and a FASTQ file with the read/qual sequences. Is there a tool to add seq to BAM? for @sjackman https://twitter.com/sjackman/status/575368165531611136 | | | |
|---|
| biostar234230 | Sliding Window : discriminate partial and fully contained fragments (from a bam file) | | | |
|---|
| biostar251649 | Annotating the flanking bases of SNPs in a VCF file | vcf annotation sequence reference | | |
|---|
| vcfbedsetfilter | Set FILTER for VCF if intersects with BED. | vcf bed filter | | |
|---|
| bamliftover | Lift-over a BAM file. | bam liftover | | |
|---|
| blast2sam | Convert a **BLASTN-XML** input to SAM | sam blast | | |
|---|
| reduceblast | Reduce the size of XML blast, by removing iterations that have no Hit | blast xml | | |
|---|
| blastn2snp | print indel/mismatch in a blastn stream | blast snp | | |
|---|
| splitbam3 | Split a BAM by chromosome group | sam bam split | | |
|---|
| vcfindextabix | Index and sort a VCF on the fly with Tabix | vcf tabix | | |
|---|
| blastfilterjs | Filters a BlastOutput with a javascript expression. The script injects each <Hit> as the variable 'blasthit'. The user script should return 'true' to keep the hit. | blast js javascript filter | | |
|---|
| SamSlop | extends sam by 'x' bases using the reference sequence | sam bam | | |
|---|
| vcfgenesplitter | Split VCF+VEP by gene/transcript. | genes vcf | | |
|---|
| sammaskalignedbases | Mask bases aligned on Reference. | | | |
|---|
| queue2make | Convert Broad/Queue genomestrip Log stream to Makefile. | | | |
|---|
| pcrclipreads | Soft clip bam files based on PCR target regions | sam bam pcr bed | | |
|---|
| vcfmovefilterstoinfo | Move any FILTER to the INFO column. reset FILTER to PASS | vcf format info | | |
|---|
| vcfburdenmaf | MAF for Cases / Controls | vcf burden maf case control | | |
|---|
| vcfburdenfisherh | Fisher Case /Controls per Variant | vcf burden fisher | | |
|---|
| vcfinjectpedigree | Injects a pedigree (.ped) file in the VCF header | vcf pedigree burden | | |
|---|
| samcolortag | Add the UCSC 'YC' color tag in a BAM. See http://software.broadinstitute.org/software/igv/book/export/html/6 and http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html | sam bam metadata javascript igv visualization | | |
|---|
| vcffilternotinpedigree | Adds a FILTER 'NotInPedigree' if the only not(homref) genotypes are not in a pedigree | burden vcf pedigree | | |
|---|
| vcfburdenexac | Burden filter 3 - Exac | vcf burden exac | | |
|---|
| vcf2table | convert a vcf to a table, to ease display in the terminal | vcf table visualization | | |
|---|
| allelefreqcalc | Allele Frequency Calculator | vcf af | | Use bioalcidae. |
|---|
| bamindexreadnames | Build a dictionary of read names to be searched with BamQueryReadNames | | | |
|---|
| bamtreepack | Create a TreeMap from one or more SAM/BAM file. Ouput is a SVG file. | bam treepack | | |
|---|
| fastqrecordtreepack | Create a TreeMap from one or more Fastq file. Ouput is a SVG file | | | |
|---|
| samfindclippedregions | Fins clipped position in one or more bam. | sam bam clip vcf | | |
|---|
| vcftreepack | Create a TreeMap from one or more VCF. Ouput is a SVG file. | | | |
|---|
| vcfburdensplitter | Split VCF Using a Burden Splitter (by gene, transcript, etc..) | | | |
|---|
| vcfburdenfisherv | Fisher Case / Controls per Variant (Vertical) | vcf burden fisher | | |
|---|
| vcfburdenrscriptv | Fisher Case / Controls per Variant (Vertical) | vcf burden fisher | | |
|---|
| vcfderby01 | Insert similar VCFs into an Apache Derby Database | vcf sql derby burden | | |
|---|
| vcfdoest | generate Transcript information for DOEST test | vcf burden doest | | |
|---|
| bioalcidae | javascript version of awk for bioinformatics | sam bam vcf javascript js nashorn | | |
|---|
| picardmetrics2xml | transforms a picard metrics file to XML. See http://plindenbaum.blogspot.fr/2013/02/making-use-of-picard-metrics-files.html | picard xml metrics | | |
|---|
| casectrlcanvas | draw a chart of case/control maf from a stream of X/Y values | vcf case control visualization jfx chart maf | | |
|---|
| lowresbam2raster | Low Resolution BAM to raster graphics | bam alignment graphics visualization png gtf | | |
|---|
| Query a Bam file indexed with BamIndexReadNames | | | |
|---|
| knime2txt | converts a Knime Workflow to a html representation. | knime workflow convert | | |
|---|
| lumpyvcf2circos | Lumpy to Circos | lumpy circos sv vcf | | |
|---|
| genscan | Paint a Genome Scan picture from a Tab delimited file (CHROM/POS/VALUE1/VALUE2/....). | chromosome reference chart visualization | | |
|---|
| vcfucsc | annotate an VCF with mysql UCSC data | ucsc mysql vcf | | |
|---|
| xsltstream | XSLT transformation for large XML files. xslt is only applied on a given subset of nodes. | xml xslt xsl stylesheet | | |
|---|
| vcfloopovergenes | Generates a BED file of the Genes in an annotated VCF, loop over those genes and generate a VCF for each gene, then execute an optional command. | vcf gene burden | | |
|---|
| vcffilterjdk | Filtering VCF with dynamically-compiled java expressions | vcf filter java jdk | | |
|---|
| optimizer | Genetic-Programming-like parameters optimizer | genetic-programming | | |
|---|
| bioalcidaejdk | java-based version of awk for bioinformatics | sam bam vcf java jdk gtf | | |
|---|
| copynumber01 | experimental CNV detection. | cnv bam sam | | |
|---|
| samjdk | Filters a BAM using a java expression compiled in memory. | sam bam java jdk filter | | |
|---|
| vcfmakedict | Create a SAM Sequence Dictionary from a set of VCF files. | vcf dict fai | | |
|---|
| vcfbigwig | Annotate a VCF with values from a bigwig file | vcf wig wiggle bigwig | | |
|---|
| vcfnocall2homref | Convert the UNCALLED gentoypes in a VCF to HOM_REF. This tool can be used after using GATK CombineVariants. | vcf | | use bcftools plugin: +setGT. |
|---|
| gff2kg | Convert GFF3 format to UCSC knownGene format. | gff ,gtf knownGene ucsc convert | | |
|---|
| minicaller | Simple and Stupid Variant Caller designed for @AdrienLeger2 | bam sam calling vcf | | |
|---|
| vcfoptimizeped4skat | Optimize ped file for SKAT | vcf pedigree skat burden | | |
|---|
| vcfskatslidingwindow | SkatFactory Over genome using a sliding window. | vcf pedigree skat burden | | |
|---|
| vcfskat | Calculate SKAT score for a VCF. | vcf pedigree skat burden | | |
|---|
| vcfserver | Web Server displaying VCF file. A web interface for vcf2table | vcf table visualization server web | | |
|---|
| tviewserver | Web Server displaying SAM/BAM file. A web interface for jvarkit:tview | sam bam table visualization server web | | |
|---|
| pubmedgraph | Creates a Gephi-gexf graph of references-cites for a given PMID | pubmed xml graph | | |
|---|
| vcftrap | annotate vcf with trap database http://trap-score.org/ | vcf trap annotation | | |
|---|
| trapindexer | Convert text data to binary format for the trap DATABASE database http://trap-score.org/. Those data can be used by the tool `vcftrap`. | trap | | |
|---|
| prettysam | Pretty SAM alignments | sam bam | | |
|---|
| vcfremoveunusedalt | Remove unused ALT allele if there is no genotype with this alt, or there is no sample but AC=0 | vcf genotype | | |
|---|
| variantsinwindow | Annotate Number of Variants overlaping a sliding window. | vcf annotation | | |
|---|
| samaddpi | Add predicted median insert size 'PI' to SAM Read groups (RG). | sam bam | | |
|---|
| goutils | Gene Ontology Utils. Retrieves terms from Gene Ontology | geneontology go gexf | | |
|---|
| indexcovjfx | display indexcov data in a jfx client | cnv jfx duplication deletion sv | | |
|---|
| indexcov2vcf | convert indexcov data to vcf | cnv duplication deletion sv indexcov | | |
|---|
| tview | equivalent of samtools tview | sam bam visualization terminal | | |
|---|
| samcustomsortjdk | Sort a BAM file using a java expression compiled at runtime. | sam bam java jdk sort | | |
|---|
| simpleplot | simple figure plotter output is a R script | char figure | | |
|---|
| cytoband2svg | Creates a svg karyotype . | karyotype svg ideogram | | |
|---|
| vcfstatsjfx | VCF statistics | vcf stats | | |
|---|
| vcfancestralalleles | Annotate a VCF with it's ancestral allele. Data from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/human_ancestor_GRCh37_e59.README | vcf ancestral 1000k allele | | |
|---|
| vcfgo | Find the GO terms for VCF annotated with SNPEFF or VEP | vcf go | | do not use this. |
|---|
| vcfcomparecallersonesample | For my colleague Julien: VCF with one sample called using different callers. Only keep variant if it was found in min<x=other-files<=max | vcf compare | | |
|---|
| bednonoverlappingset | Split a Bed file into non-overlapping data set. | bed | | |
|---|
| vcfafinfofilter | Filter VCF annotated with external (AF or AC/AN) frequency information like vcfgnomad | vcf annotation af | | |
|---|
| biostar322664 | Extract PE Reads (with their mates) supporting variants in vcf file | sam bam vcf | | |
|---|
| vcfcomposite | (in developpement) Finds Variants involved in a Het Compound Disease | vcf disease annotation pedigree haplotype | | |
|---|
| biostar92368 | Binary interactions depth. | protein interaction interactome | | |
|---|
| wescnvsvg | SVG visualization of bam DEPTH for multiple regions | bam alignment graphics visualization svg wes bed capture exome | | |
|---|
| naivecnvdetector | experimental CNV detection for multiple samples. | cnv bam sam wig bigwig bigbed | | |
|---|
| vcfclusteredreadedge | Variant annotation : variants clustered near the ends of reads | sam bam vcf | | |
|---|
| biostar332826 | Fast Extraction of Variants from a list of IDs | vcf rs id | | |
|---|
| pubmedauthorgraph | Creates a graph from Pubmed and Authors | pubmed ncbi graph | | |
|---|
| gephicmd | Cmd-line oriented for gephi. | graph gexf gephi visualization | | |
|---|
| gexftr | Gexf file manipulation | gexf graph network | | |
|---|
| ncbigenedump | Dump XML results from a list of gene using NCBI/Eutils | ncbi gene xml | | |
|---|
| vcfallelebalance | Insert missing allele balance annotation using FORMAT:AD | vcf allele-balance depth | | |
|---|
| vcfgapfrequent | Filter VCF annotated with external (AF or AC/AN) frequency information like vcfgnomad | vcf | | |
|---|
| biostar336589 | displays circular map as SVG from BED and REF file | genome browser circular bed svg | | |
|---|
| bamslicebed | For @wouter_decoster : slice (long reads) overlapping the records of a BED file | sam bam bed | | |
|---|
| mergecnvnator | Merge CNVNator results | cnv indel cnvnator | | |
|---|
| faidxsplitter | Split bed of reference genome into overlapping parts | vcf reference bed | | |
|---|
| cnvtview | Text visualization of bam DEPTH for multiple regions in a terminal | bam alignment graphics visualization cnv ascii text | | |
|---|
| sv2svg | BAM to SVG. Used to display structural variations. | bam alignment graphics visualization svg structural variant | | |
|---|
| vcf2bed | vcf to bed | bed vcf | | |
|---|
| biostar352930 | Fills the empty SEQ(*) and QUAL(*) in a bam file using the the reads with the same name carrying this information. | sam bam | | |
|---|
| pubmed404 | Test if URL in the pubmed abstracts are reacheable. | pubmed url | | |
|---|
| vcfstrechofgt | Try to finds deletion by searching strech of HOM_REF/HOM_VAR/NO_CALL Genotypes. | vcf deletion cnv | | |
|---|
| haloplexparasite | for @SolenaLS : remove artctifacts from haloplex that gives indels in GATK hapcaller | vcf haloplex | | |
|---|
| ngsfilesscanner | Build a persistent database of NGS file. Dump as XML. | ngs bam sam vcf xml | | |
|---|
| vcfburdensplitter2 | new version | vcf burden gene vep snpeff prediction | | |
|---|
| vcfensemblreg | Annotate a VCF with the UCSC genome hub tracks for Ensembl Regulation. | vcf ensembl regulation | | |
|---|
| scanretrocopy | Scan BAM for retrocopies | sam bam cigar clip sv retrocopy | | |
|---|
| sigframe | SigFrame displays CGH/ position+values in a GUI | cgh gui visualization | | |
|---|
| samviewwithmate | Extract reads within given region(s), and their mates | sam bam | | |
|---|
| kg2fa | convert ucsc genpred to fasta | kg knownGene fasta genpred | | |
|---|
| vcfscanupstreamorf | Scan BAM for upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs | vcf uorf | | |
|---|
| vcfgnomadpext | Peek annotations from gnomadpext | vcf annotation gnomad | | |
|---|
| vcfsparql | Query RDF with Sparql. Very slow. Just a proof of concept | vcf sparql rdf arq semanticweb | | |
|---|
| samtranslocations | Explore balanced translocations between two chromosomes using discordant paired-end reads. | sam bam sv translocation | | |
|---|
| convertliftoverchain | Convert the contigs in a liftover chain to match another REFerence. (eg. to remove chr prefix, unknown chromosomes etc...) | chain liftover | | |
|---|
| mkminibam | Creates an archive of small bams with only a few regions. | bam sam | | |
|---|
| vcfdistancevariants | Annotate variants with the distance between previous and next variant. | vcf annotation distance | | |
|---|
| hicfileinfo | Prints information about a HI-C File/URL | hic | | |
|---|
| vcfwindowsplitter | Split VCF by sliding window | vcf sliding window | | |
|---|
| bammatrix | Bam matrix, inspired from 10x/loupe | sam bam compare matrix | | |
|---|
| vcfphased01 | X10 Phased SVG to Scalar Vector Graphics (SVG) | x10 phased genotypes svg | | |
|---|
| starretrocopy | Scan retrocopies from the star-aligner/bwa output | sam bam cigar clip sv retrocopy star | | |
|---|
| ijgv2vcf | Convert zips of Integrative Japanese Genome Variation to VCF file. | vcf jgvd japan tommo | | Deprecated since data are now available as VCF. |
|---|
| vcfadfraction | filter VCF for strange FORMAT:AD fraction | vcf allele-balance depth | | |
|---|
| gtfsplitter | Split GTF file per gene, transcript, chromosome... | gtf | | |
|---|
| gtfretrocopy | Scan retrocopies by comparing the gtf/intron and the deletions in a VCF | gtf retrocopy deletion | | |
|---|
| vcfgnomadsv | Peek annotations from gnomad structural variants | vcf annotation gnomad sv | | |
|---|
| knownretrocopy | Annotate VCF structural variants that could be intron from retrocopies. | gtf retrocopy deletion | | |
|---|
| gtfliftover | LiftOver GTF file. | gtf liftover | | |
|---|
| scansv | Scan structural variants for case/controls data | cnv indel sv pedigree | | |
|---|
| bamheteroplasmy | Call a VCF for the Mitochondria (Experimental) | vcf sam bam mitochondria | | |
|---|
| findhtsfiledict | Scan a set of HTS files (VCF, BAM, CRAM), return a tab delimited file (path-of-file,path-to-fasta) | sam bam cram vcf dict | | |
|---|
| biostar398854 | Extract every CDS sequences from a VCF file | vcf gtf | | |
|---|
| psl2bam | Convert PSL to SAM/BAM | blat sam bam psl pslx | | |
|---|
| mantamerger | Merge Vcf from Manta VCF. | sv burden manta vcf | | |
|---|
| vcfburdenslidingwindow | Run Burden Sliding window | vcf burden case control | | |
|---|
| depthofcoverage | A custom 'Depth of Coverage'. | depth bam sam coverage | | |
|---|
| biostar404363 | introduce artificial mutation SNV in bam | sam bam variant | | |
|---|
| hmmmergebed | For @154sns. Merge hmm bed | bed merge | | |
|---|
| vcfrebase | Restriction sites overlaping variations in a vcf | vcf rebase restriction enzyme | | |
|---|
| vcfgtfsplitter | Split VCF+VEP by gene/transcript using a GTF file. | genes vcf split gtf | | |
|---|
| vcfpeekaf | Peek the AF from another VCF | vcf annotation af | | |
|---|
| plotsashimi | Print Sashimi plots from Bam | bam visualization svg rna exon rnaseq | | |
|---|
| bamwithoutbai | Query a Remote BAM without bai | bam sam bai remote | | |
|---|
| bedcluster | Clusters a BED file into a set of BED files. | bed chromosome contig | | |
|---|
| coverageserver | Jetty Based http server serving Bam coverage. | cnv bam coverage server | | |
|---|
| fastqsplit | Split Fastq files into multiple files. | fastq | | |
|---|
| bedmergecnv | Merge Bed records if they overlap a fraction of their lengths. | bed chromosome contig | | |
|---|
| validatecnv | Experimental CNV Genotyping. Look variance of depths before/after putative known CNV. | cnv bam sam vcf depth | | |
|---|
| htsfileserver | Jetty Based http server serving Vcf and Bam files. | vcf bam server | | |
|---|
| breakdancer2vcf | Convert output of breakdancer to VCF | cnv sv breakdancer vcf | | |
|---|
| indexcov2sv | same as indexcov2vcf but merge segments | cnv duplication deletion sv indexcov | | |
|---|
| vcfpostprocesssv | Postprocess BND pairs in a MANTA/LUMPY-SV. | cnv sv gidss vcf | | |
|---|
| coverageplotter | Display an image of depth to display any anomaly an intervals+bams | cnv bam depth coverage svg | | |
|---|
| bamallelebalance | Compute statistics about allele balance from a set of Bams | vcf allele-balance depth bam | | |
|---|
| vcfpar | Flag human sexual regions excluding PAR. | vcf sex par | | |
|---|
| combinevcffisher | Combine multiple VCF to perform a 'vertical' fisher test. | vcf burden fisher | | |
|---|
| vcfbraiding | visualization for variants and attributes using https://visdunneright.github.io/sequence_braiding/docs/ . | vcf visualization | | |
|---|
| vcfspliceai | Annotate VCF with spiceai web service | vcf splice splicing spliceai | | |
|---|
| wgscoverageplotter | Whole genome coverage plotter | svg bam depth coverage | | |
|---|
| biostar480685 | paired-end bam clip bases outside insert range | sam bam clip | | |
|---|
| kg2gff | Convert UCSC genpred file to gff3 | gff gff3 ucsc genpred | | |
|---|
| biostar489074 | call variants for every paired overlaping read | sam bam vcf call | | |
|---|
| expansionhuntermerge | Merge Vcf from ExpansionHunter. | vcf merge ExpansionHunter | | |
|---|
| bamphased01 | Extract Reads from a SAM/BAM file supporting at least two variants in a VCF file. | vcf phased genotypes bam | | |
|---|
| vcfstrech2svg | another VCF to SVG | vcf deletion cnv svg | | |
|---|
| biostar497922 | Split VCF into separate VCFs by SNP count | vcf | | |
|---|
| biostar9462889 | Extracting reads from a regular expression in a bam file | sam bam split util | | |
|---|
| swingbamcov | Bam coverage viewer using Java Swing UI | bam alignment graphics visualization swing | | |
|---|
| swingvcfview | VCFviewer using Java Swing UI | vcf visualization swing | | |
|---|
| bamxtremdepth | Compute low and high depth shared by a set of BAM files | bam depth coverage | | |
|---|
| biostar9469733 | Extract reads mapped within chosen intronic region from BAM file | sam bam rnaseq bed | | |
|---|
| vcffilterbyliftover | Add FILTER(s) to a variant when it is known to map elsewhere after liftover. | vcf liftover | | |
|---|
| builddbsnp | Build a DBSNP file from different sources for GATK | vcf dbsnp | | |
|---|
| iranomescrapper | Iranome scrapper | iranome vcf | | |
|---|
| ukbiobanksamples | Select samples from ukbiobank | ukbiobank | | |
|---|
| findgvcfsblocks | Find common blocks of calleable regions from a set of gvcfs | gvcf gatk vcf | | |
|---|
| rnaseqpolya | find poly-A tail in RNASeq data | bam sam rnaseq polya | | |
|---|
| bam2haplotypes | Reconstruct SNP haplotypes from reads | vcf phased genotypes bam | | |
|---|
| mergesv | Experimental SV/CNV merger. | cnv indel sv | | |
|---|
| vcf2intervals | split a vcf to interval or bed for parallelization | vcf bed interval | | |
|---|
| vcfroh | VCF ROH | vcf roh | | |
|---|
| biostar9501110 | Keep reads including/excluding variants from VCF | sam bam vcf | | |
|---|
| vcfbigbed | Annotate a VCF with values from a bigbed file | vcf wig wiggle bigbed bed | | |
|---|
| setfiletools | Utilities for the setfile format | setfile bed | | |
|---|
| fastqsw | align fasta sequences vs fastq | fastq align sw | | |
|---|
| swingvcfjexl | Filter VCF using Java Swing UI and JEXL/Javascript expression | vcf visualization swing jexl javascript | | |
|---|
| basecoverage | 'Depth of Coverage' per base. | depth bam sam coverage vcf | | |
|---|
| bam4indexcov | prepare BAM/CRAM from indexcov. | cnv duplication deletion sv | | can be replace with samtools view. See doc. |
|---|
| swingindexcov | indexcov visualization | cnv duplication deletion sv | | |
|---|
| manhattan | Manhattan plot SVG picture from different sources. | chromosome reference chart visualization svg | | |
|---|
| uniprot2svg | plot uniprot to SVG | uniprot svg | | |
|---|
| gtf2bed | Convert GTF/GFF3 to BED. | gtf gff gff3 bed | | |
|---|
| texbam | Write text in a bam. Mostly for fun... | fun bam sam txt | | |
|---|
| gff3upstreamorf | Takes a ucsc genpred file, scan the 5' UTRs and generate a GFF3 containing upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs | gff gff3 uorf uorf | | |
|---|
| vcfsamplesprs | another program for @AntoineRimbert | vcf indel | | |
|---|
| vcfsplitnvariants | Split VCF to 'N' VCF files | vcf | | |
|---|
| samrmdupnames | remove duplicated names in sorted BAM | sam bam | | |
|---|
| oboutils | OBO Ontology Utils. | obo ontology | | |
|---|
| swingbamview | Read viewer using Java Swing UI | bam alignment graphics visualization swing | | |
|---|
| gtexrs2qtl | extract gtex eqtl data from a list of RS | gtex rs eqtl sqtl | | |
|---|
| sv2fasta | convert VCF of structural variant(s) to fasta for pggb | vcf cnv fasta | | |
|---|
| vcfgatkeval | Eval/Plot gatk INFO tags for filtering | vcf gatk | | |
|---|
| bio2rdf | Build a RDF database for human from misc sources | rdf ontology sparql | | |
|---|
| vcfgrantham | add grantham score from annotated VCF variant | vcf grantham | | |
|---|
| htsfreemarker | Apply Freemarker to VCF/BAM/JSON files. | template freemarker vcf bam | | |
|---|
| rdcombine | Substract/Add RDF models | | | |
|---|
| rdfcombine | Substract/Add RDF models | | | |
|---|
