hall-lab

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cluster_intro

 2  0
Hall Lab Computing 101

sv_paper_042020

 2  1
supplementary data for abel et al paper
C

speedseq

 300  115
A flexible framework for rapid genome analysis and interpretation

lumpy-sv

 0  1
lumpy: a general probabilistic framework for structural variant discovery

soup

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

fastqtl

 4  10
Fork of FastQTL for SVs
Python

svtools

 125  55
Tools for processing and analyzing structural variants.

svtyper

 107  53
Bayesian genotyper for structural variants

gtex

 18  8
GTEx analysis scripts

long-read-validation

 9  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

bamkit

 2  5
Tools for common BAM file manipulations

cromwell-deployment

 2  4
Scripts and configuration to setup a Cromwell deployment

assembly_validation

 1  1

cshl_sv_2016

 1  0

io

 1  0
i/o tools

lumpy-merge

 1  0

old-laims

 0  1
Shell

protocols

 2  0
Hall lab analysis protocols
wdl

sv-pipeline

 38  19
Pipeline for structural variation detection in cohorts

competitive-alignment

 3  2

gatk4-germline-snv-pipeline

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