Ira Hall lab

speedseq

A flexible framework for rapid genome analysis and interpretation

svtools

Tools for processing and analyzing structural variants.

svtyper

Bayesian genotyper for structural variants

sv-pipeline

Pipeline for structural variation detection in cohorts

gtex

GTEx analysis scripts

competitive-alignment

long-read-validation

Long-read validation of BEDPE structural variation

fastqtl

Fork of FastQTL for SVs

1kg_sv_comparison

assembly_validation

extract_sv_reads

Tool for extracting splitter or discordant reads from a BAM or CRAM file.

sv_paper_042020

supplementary data for abel et al paper

bamkit

Tools for common BAM file manipulations

cluster_intro

Hall Lab Computing 101

cromwell-deployment

Scripts and configuration to setup a Cromwell deployment

cshl_sv_2016

gatk4-germline-snv-pipeline

GATK4 pipeline for joint variant calling (SNP/INDELs)

io

i/o tools

tenx-gcp

Run 10X Genomics Software in Google Cloud Deployments

ArrowGrid

CADD-scripts

CADD scripts release for offline scoring. For more information about CADD, please visit our website

cloud-polices

crimson

Bioinformatics tool outputs converter to JSON or YAML

cromulent

FinnSV_paper_1220

The summary statistics of FinMetSeq SV paper

lah

Local Assembly of Haplotypes

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

old-laims

pipelines-api-examples

Examples for the Google Genomics Pipelines API.

soup

Catch-all for uncategorized or project-specific scripts 🍵