Search Results for "maf"

vcf2maf is a Perl-based tool developed by the Memorial Sloan Kettering Cancer Center to convert Variant Call Format (VCF) files into Mutation Annotation Format (MAF) files. This conversion standardizes variant annotations, facilitating downstream analyses in cancer genomics. ​

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. -ni option added. -vb option (-B in varscan) added exac03nontcga is added. An error about VARSCAN is corrected. Mutlithreading for dbsnp annotation, Haplotypecaller, Varscan and bamreadcount more efficient. ...

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.

...***Update*** The genelist file reports those with p<0.05 only. Now the script incorporates genvisr. hg38 option is added. md (most deleterous) option is added. A script to transform TCGA MAF file is provided.

...For data exploration and dimensionality reduction, it includes multivariate methods common in the ToF-SIMS community: PCA (Principal Component Analysis), MCR (Multivariate Curve Resolution), MAF (Maximum Autocorrelation Factors), and MNF (Minimum Noise Fraction). It also interoperates with Bioconductor’s imaging stack (e.g. EBImage) so users can apply segmentation and image analysis operations on mass images.

A reworking in C++ of KBMAG. A package and C++ library for computing automatic structures and confluent rewriting system for group and coset rewriting systems, and for computing with finite state automata

...The new markers are generated according to real local data characteristics, modeled statistically, and are interpolated locally between real markers in the data. The function allows the user to specify a desired level of marker density, with a minor allele frequency (MAF) limit, which is produced in a reasonable computation time. Reference: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0830-7

Trinity is mobile agent framework for creation of wide range of mobile agent types. Main goal of project is to provide a tool for rapid development of non-complex agents. Trinity is implemented in .NET v3.5 with usage of Windows Workflow Foundation and W

A personal genealogy/family history application for Mac OS X and iPhone, modelled after a previous version of PAF for Macintosh called Family Records. This is intended to be easy to learn for newer users and to be familiar to previous users of Family Rec