talkowski-lab Goto Github PK

1kgp-gatk-sv-test

Test GATK-SV on 1KGP Subset

1kgp_alignment_instructions

athena

Toolkit for structural variation mutation rates and dosage sensitivity

bamstat

Categorization of discordant read pairs into SV types

bpp3

Primer script

cnv-validation

commonmind-sv

count_variant_occurrence

dsmap

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

gatk4-exome-analysis-pipeline

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

gcnv-analysis-tools

Analysis tools for gCNV

gcnv-qc-update

Update to the gCNV QC step

gnomad-sv-pipeline

Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)

gnomad-sv-v3-qc

Fork of GATK-SV repo from June 10, 2021, for gnomAD-SV v3 filtering, QC, and post-processing

holmes

Pipeline for structural variation detection from liWGS libraries

plotcritic

Python deployment tool for bespoke image curation projects, oriented toward scientific projects. Please cite https://academic.oup.com/gigascience/article/7/7/giy064/5026174

pzm

rcnv2

Aggregation and analyses of rare CNVs across diseases

rwgcna

Resampled consensus WGCNA

smc_cnn_model

Pipelines to reproduce analysis result for the SMC new target paper

sv-adjudicator

sv_callers

sv_callers_snakemake

svtk

tada_2022

variant-interpretation

wgd

A suite of tools to evaluate dosage in whole-genome sequencing libraries