Talkowski Laboratory

Talkowski Laboratory at Massachusetts General Hospital & The Broad Institute

Pinned Repositories

1KGP_alignment_instructions
10
gnomad-sv-pipeline
Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
Language:R36 13 414
Holmes
Pipeline for structural variation detection from liWGS libraries
Language:Shell5 15 00
pzm
Language:Python10
rCNV2
Aggregation and analyses of rare CNVs across diseases
Language:R14 3 13
rWGCNA
Resampled consensus WGCNA
Language:R21
SMC_CNN_Model
Pipelines to reproduce analysis result for the SMC new target paper
Language:Python10
SV-Adjudicator
Language:Python25 10 25
svtk
Language:Python35 24 2612
variant-interpretation
Language:WDL45

Talkowski Laboratory's Repositories

talkowski-lab/gnomad-sv-pipeline
Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
Language:R36 13 414
talkowski-lab/svtk
Language:Python35 24 2612
talkowski-lab/SV-Adjudicator
Language:Python25 10 25
talkowski-lab/rCNV2
Aggregation and analyses of rare CNVs across diseases
Language:R14 3 13
talkowski-lab/Holmes
Pipeline for structural variation detection from liWGS libraries
Language:Shell5 15 00
talkowski-lab/variant-interpretation
Language:WDL45
talkowski-lab/rWGCNA
Resampled consensus WGCNA
Language:R21
talkowski-lab/1KGP_alignment_instructions
10
talkowski-lab/pzm
Language:Python10
talkowski-lab/SMC_CNN_Model
Pipelines to reproduce analysis result for the SMC new target paper
Language:Python10
talkowski-lab/TADA_2022
Language:R1 6 13
talkowski-lab/athena
Toolkit for structural variation mutation rates and dosage sensitivity
Language:Python0 4 20
talkowski-lab/cnv-validation
Language:WDL0 5 01
talkowski-lab/count_variant_occurrence
Language:WDL0 3 01
talkowski-lab/dsmap
Language:Shell0 4 21
talkowski-lab/1kgp-gatk-sv-test
Test GATK-SV on 1KGP Subset
Language:WDL
talkowski-lab/bamstat
Categorization of discordant read pairs into SV types
Language:C++23 0
talkowski-lab/bpp3
Primer script
Language:Python3 01
talkowski-lab/CommonMind-SV
Language:Shell
talkowski-lab/gatk4-data-processing
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
Language:wdl
talkowski-lab/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.
Language:wdl1
talkowski-lab/gatk4-germline-snps-indels
Workflows for germline short variant discovery with GATK4
talkowski-lab/gCNV-analysis-tools
Analysis tools for gCNV
Language:R1
talkowski-lab/gCNV-QC-Update
Update to the gCNV QC step
Language:R
talkowski-lab/gnomad-sv-v3-qc
Fork of GATK-SV repo from June 10, 2021, for gnomAD-SV v3 filtering, QC, and post-processing
Language:wdl
talkowski-lab/outlier-exclusion
Workflows for filtering gATK-SV callsets
Language:WDL
talkowski-lab/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
Language:Shell
talkowski-lab/SV_callers
Language:wdl
talkowski-lab/SV_Callers_Snakemake
Language:Python
talkowski-lab/WGD
A suite of tools to evaluate dosage in whole-genome sequencing libraries
Language:R