Pinned Repositories
Bestie
wdl hts-analysis
DigitalBarcodeReadgroups
Create readgroups from barcodes with random nucleotides incorporates into them. This is a git for noting down the results.
fastqtl
Enhanced version of the FastQTL QTL mapper
mmterpstra's Repositories
mmterpstra/Bestie
wdl hts-analysis
mmterpstra/BurnDown
Scrum burndown chart misc scripts
mmterpstra/cluster-utils
Collection of utilities / helper scripts to make life easier on our HPC clusters.
mmterpstra/CoNVaDING_reload
Fork of the CoNVaDING software - Copy Number Variation Detection In NGS Gene panels was designed for small (single-exon) copy number variation (CNV) detection in high coverage NGS data.
mmterpstra/depad-utils
Utilities for deploy admins
mmterpstra/DiverseScripts
mmterpstra/easybuild-easyconfigs
A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
mmterpstra/Ericscript
ChimERIC TranSCRIPT detection
mmterpstra/fgbio
Tools for working with genomic and high throughput sequencing data.
mmterpstra/fusioncatcher
Somatic fusion genes finder for RNA-seq data
mmterpstra/gatk4-data-processing
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
mmterpstra/gsport
mmterpstra/HTS_Galaxy
Files for Galaxy tutorial
mmterpstra/ichorCNA
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
mmterpstra/marktrimming
cutadapt integration in gatk pipline
mmterpstra/mirdeep2
Discovering known and novel miRNAs from small RNA sequencing data
mmterpstra/miRWDL
miRWDL scalable mirna qualitfication on the wdl
mmterpstra/molgenis-c5-TumorNormal
mmterpstra/mrmosaic
MrMosaic (Genomic Mosaic Structural Variant Caller)
mmterpstra/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
mmterpstra/NextFlexMirDeep2
mmterpstra/NGS_DNA
NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC
mmterpstra/pipeline-util
Misc tools for pipelines written for variant detection (GATK picard BWA SAMtools) with molgenis-compute-5.
mmterpstra/randfold
Permutation test for microRNA precursor sequences.
mmterpstra/startmoduletut
wip tutorial how to start a module
mmterpstra/TableToXlsx
Convert your text based tables to excel format / Minimal example of the Excel::Writer::XLSX module in perl.
mmterpstra/take-it-easyconfigs
mmterpstra/tasks
A collection of reusable WDL tasks. Category:Other
mmterpstra/VIS
HGVS Variant interpretation using SPLICEAI
mmterpstra/wdl
Workflow Description Language - Specification and Implementations