Ira Hall lab

bamkit

Tools for common BAM file manipulations

competitive-alignment

cromulent

speedseq

A flexible framework for rapid genome analysis and interpretation

assembly_validation

svtools

Tools for processing and analyzing structural variants.

cromwell-deployment

Scripts and configuration to setup a Cromwell deployment

sv-pipeline

Pipeline for structural variation detection in cohorts

lah

Local Assembly of Haplotypes

cloud-polices

svtyper

Bayesian genotyper for structural variants

tenx-gcp

Run 10X Genomics Software in Google Cloud Deployments

FinnSV_paper_1220

The summary statistics of FinMetSeq SV paper

gatk4-germline-snv-pipeline

GATK4 pipeline for joint variant calling (SNP/INDELs)

CADD-scripts

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

sv_paper_042020

supplementary data for abel et al paper

old-laims

cluster_intro

Hall Lab Computing 101

ArrowGrid

crimson

Bioinformatics tool outputs converter to JSON or YAML

fastqtl

Fork of FastQTL for SVs

extract_sv_reads

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

1kg_sv_comparison

long-read-validation

Long-read validation of BEDPE structural variation

soup

Catch-all for uncategorized or project-specific scripts 🍵

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

pipelines-api-examples

Examples for the Google Genomics Pipelines API.

gtex

GTEx analysis scripts

cshl_sv_2016

io

i/o tools