hall-lab

C

speedseq

268 97
A flexible framework for rapid genome analysis and interpretation

lumpy-sv

0 0
lumpy: a general probabilistic framework for structural variant discovery

soup

0 2
Catch-all for uncategorized or project-specific scripts 🍵

C++

fastqtl

3 9
Fork of FastQTL for SVs

Python

svtools

85 39
Tools for processing and analyzing structural variants.

svtyper

83 40
Bayesian genotyper for structural variants

gtex

14 8
GTEx analysis scripts

long-read-validation

7 3
Long-read validation of BEDPE structural variation

extract_sv_reads

4 0
Tool for extracting splitter or discordant reads from a BAM or CRAM file.

1kg_sv_comparison

3 1

cromwell-deployment

2 2
Scripts and configuration to setup a Cromwell deployment

bamkit

1 3
Tools for common BAM file manipulations

cshl_sv_2016

1 0

io

1 0
i/o tools

CADD-scripts

0 0
CADD scripts release for offline scoring. For more information about CADD, please visit our website

cloud-polices

0 0

crimson

0 0
Bioinformatics tool outputs converter to JSON or YAML

cromulent

0 0

cshl_sv_2014

0 0
CSHL structural variation demo 2014

lah

0 0
Local Assembly of Haplotypes

laims

0 1

lumpy-merge

0 0

old-laims

0 1

pipelines-api-examples

0 0
Examples for the Google Genomics Pipelines API.

tenx-gcp

0 0
Run 10X Genomics Software in Google Cloud Deployments

R

MatrixEQTL

0 0
MatrixEQTL: Ultra fast eQTL analysis via large matrix operations

Shell

protocols

1 0
Hall lab analysis protocols

ArrowGrid

0 0

assembly_validation

0 0

wdl

sv-pipeline

24 15
Pipeline for structural variation detection in cohorts

gatk4-germline-snv-pipeline

1 1
GATK4 pipeline for joint variant calling (SNP/INDELs)