Command-line toolkit for genomic datasets.
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Updated
Aug 20, 2019 - Haskell
Command-line toolkit for genomic datasets.
A Haskell script for creating input files for bam-readcount from ensembl-vep output and variant-calling format (vcf) files.
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
Analysis of paired tumor-normal whole exome sequencing data generated in a pilot open-access study of participants in Texas.
Personalized reference editor for somatic mutation discovery
A collection of scripts documenting the parameter settings used to apply variant discovery to the exploration of Duodenal Polyposis.
A Haskell script that performs basic filtration, using a filtration string, on somatic variant data.
A Haskell script that prepares .tsv files generated from sequencing data analysis for manual review.
R package containing a R Shiny app for somatic genomic variants interpretation and a tool suite to deal with an underlying local structured database.
Empirical Bayes somatic variant calling
A Haskell script for selecting variants from a variant calling format (vcf) file based on variants present in a mgibed file.
an example open source somatic variant analysis pipeline. vLoD algorithm is also integrated.
pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data
Detect germline or somatic variants from normal or tumour/normal whole-genome, whole exome, or targeted sequencing with high performance computing.
Snakemake based workflow for analysis of dnaseq data for calling germline/somatic mutations
PhylogicNDT dockcer for clonal evolution analysis
Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples
Experiments for evaluating SECEDO, clustering tumor cells based on single cell sequencing data
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
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