Pinned Repositories
gatk
Official code repository for GATK versions 4 and up
1kgenomes-gvcfs
Scripts for creating gVCF files for 1000 genomes data using StarCluster.
azure-benchmark-scripts
Scripts used in benchmarking Sentieon DNAseq and DNAscope pipelines on Azure
bioconda-recipes
Conda recipes for the bioconda channel.
docker-actions-test
A test repository for GitHub actions
Sentieon-cwl
CWL pipelines for the Sentieon tools
sentieon-dnaseq
Sentieon DNAseq
sentieon-docker
Example Dockerfiles for use with the Sentieon software
sentieon-google-genomics
Run Sentieon pipelines on Google Cloud Platform
sentieon-scripts
Helper scripts for biological data processing from Sentieon
DonFreed's Repositories
DonFreed/1kgenomes-gvcfs
Scripts for creating gVCF files for 1000 genomes data using StarCluster.
DonFreed/docker-actions-test
A test repository for GitHub actions
DonFreed/azure-benchmark-scripts
Scripts used in benchmarking Sentieon DNAseq and DNAscope pipelines on Azure
DonFreed/bioconda-recipes
Conda recipes for the bioconda channel.
DonFreed/dnascope-longread-manuscript
DonFreed/find_denovo
A simple tool for identifying *de novo* variants from a VCF/BCF file.
DonFreed/gatk
Official code repository for GATK versions 4 and up
DonFreed/gatk-protected
Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
DonFreed/htslib
C library for high-throughput sequencing data formats
DonFreed/mosaic-from-barcodes
Detect mosaic variants using barcode information
DonFreed/mosaicism-sensitivity
DonFreed/nf-sentieon
POC Nextflow pipeline to run Sentieon software
DonFreed/NVIDIA-Clara-Parabricks-Somatic-Variant-Calling-AWS-Blog
AWS Blog (Somatic Variant Calling )
DonFreed/rust-htslib
This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
DonFreed/sds
Simple Dynamic Strings library for C
DonFreed/sentieon-google-genomics
Run Sentieon pipelines on Google Cloud Platform
DonFreed/sentieon-scripts
Helper scripts for biological data processing from Sentieon
DonFreed/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
DonFreed/submixbam
Combined mixing and subsampling for simulation of mosaic variants.
DonFreed/terraform
Terraform configuration files for the Sentieon software
DonFreed/tigger-sv
DonFreed/toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
DonFreed/variant-segregation
Add a variant segregation metric to a VCF file.