Search Results for "gatk"
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Showing 16 open source projects for "gatk"
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rna-test
script for variant calling of RNA-Seq
rna_test.sh is a shell script to run GATK best practice for variant-calling in RNAseq. It uses STAR2.5 for alignment, HaplotypeCaller to call variants, and Annovar to annotate. It also employs STAR-Fusion, Cufflinks and Stringtie FPKM, HTSeq_count and BAM-readcount. Notice: STAR_gene_read and HTSeq_count are added. exac03nontcga is added. STAR-Fusion is added. Stringtie is added. -
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exome-test
script for variant calling of Exome-Seq
exome_test.sh is a shell script to run GATK best practice and varscan for variant-calling in exomseq. It uses bwa for alignment, UnifiedGenotyper and varscan to call variants, and Annovar to annotate. It also employs DepthofCoverage and BAM-readcount. [Notice] MAF files compatible with MutSigCV are added. The Annovar filter dbnsfp30a is updated. Correction of an error in the title line of merge file. -
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A script to filter exome-seq by 1000G, ExAc, dbSNP with minimal coverage and T/N ratio. The script uses the files produced by exome_test.sh. An error is corrected. The script also produces MAF file that only includes variants detected by BOTH GATK and Varscan. A few errors are corrected.
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
...The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets. The program performs mainly 4 modules 1. Align the datasets with reference database 2. Perform the variant calling using Genome Analysis Toolkit (GATK) 3. Annotate the variant using ANNOVAR 4. Create the variant protein database Apart from the main modules, the program also supports additional functions such as 1. Download the SRA 2. Convert the SRA file to fastq file format 3. Download the annotation (ANNOVAR) database and Dry-run concept to customize the commands Executables are available at http://bioinfo-tools.com/Downloads/CusVarDB/V1.0.0/ Test dataset is available at http://bioinfo-tools.com/Downloads/CusVarDB/V1.0.0/test_dataset.rar -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
...PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. ... -
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VoltMR
Pure java NGS mapping soft run on Hadoop 2.0
...Using 100 core, VoltMR finish typical exome sample (10GB),mapping, sort, mark duplicate, local realignment in 30 minitue. It use about 10GB to 15GB RAM for each hadoop mapper and reducer. Currently, VoltMR take fastq as a input and output bam/ADAM format. For DNA mapping, GATK compatible realignment/recalbration followed after mapping. For RNA mapping, splice aware algorithm is implemented. Volt is open source, released as "LGPLv3" -
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MIPVAR
MIP VARiant calling tool
A Java application to analyse Molecular Inversion Probe sequencing data within short time. Running the pipeline requires previous installation of three general tools: BWA, GATK and Bedtools. Input: For running the pipeline you need to specify 3 arguments. An example of the command is given below. The two input files are essential to specify the sample and run configuration. The environment argument should always be set to EMPTY. A brief description of other required files can be found in the example input files (see sampleConfigExample.txt and runConfigExample.txt). ... -
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2bRAD-GATK
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
DOWNLOAD THE LATEST UPDATES FROM https://github.com/z0on/2bRAD_GATK 2bRAD is a method for cost-efficient whole-genome genotyping described in Wang et al 2012 http://www.nature.com/nmeth/journal/v9/n8/abs/nmeth.2023.html This project is about analyzing 2bRAD data using a genome reference (could be a species from the same genus). Scripts and walkthrough for: - trimming and quality filtering; - removing PCR duplicates; - mapping to genome reference; - realigning around... -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
...Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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MendelChecker
QC for variant discovery from next gen sequence in pedigrees
MendelChecker is a likelihood-based measure of Mendelian segregation of Single Nucleotide Polymorphisms (SNPs) in nuclear pedigrees. We developed this method as a quality control measure for novel variant discovery from noisy next-generation sequencing data in pedigrees, such as Restriction site-associated DNA Sequencing (RAD-seq) in non-model organisms. This method implements comparison of heterogametic vs. homogametic transmission, i.e., sex linked vs. autosomal segregation. -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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abcontamination
Plots allele balance histogram and assesses sample contamination.
...It requires that the R statistical package is installed and in your path and can be run on the Linux, Unix or Mac computer. It does not work on multi-sample VCF files. If your VCF is not annotated for AB=<num> you may do this using the Broad's GATK annotation functions, the VCF file and the sample's bam file. -
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Bis-SNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Bis-SNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. ...
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