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NGS structural variant (SV) callers

• Manta (C++/Python)

• DELLY (C++)

• LUMPY (C/C++/Python)

• GRIDSS (Java/R/Python)

• Smoove

• PINDEL (C++)

• BreakDancer (Perl/C++)

• SV2 (Python/Cython)

• Wham (C++)

• TIDDIT (C++)

• Sniffles (C/C++)

• Kevlar (INDELs only)

• SnowmanSV (C/C++)

• SMuFin - reference-free detection of SNVs and SVs

• Pindel (C++)

• GROM

• CTK

• iCallSV - using DELLY

• bcbio:sv pipeline (Python) wraps Manta, Lumpy, Delly, GRIDSS, Wham

• NextSV

• Illumina Analysis Pipeline (Perl) wraps Manta and Delly

• MetaSV (Python)

• GATK4 (Java)

• Hartwig Medical Foundation

Simulation tools/benchmarks

• 16 SV Caller benchmarks

• Pysim

• SCNVSim

• ART

• VarSim

• bamsurgeon

• SURVIVOR

• SVEngine

• wgsim

• SimSvGenomes

• http://bcb.io/2015/03/05/cancerval/

• ICGC-TCGA DREAM Mutation Calling challenge

• HuRef Variant Gold Set

• Genome in the Bottle (GIAB) - Somatic truth set

• NA12878/NA24385 tumor-like mixture (Hartwig Medical Foundation)

• 1K Genomes' NA12878 SV call set

• Somatic reference standard (COLO829)

• COSMIC

• TCGA Mutation Calling Benchmark

• Google Genomics

• GA4GH benchmarking tools

• TRUVARI

• CHM

Alignment/variant call formats

• http://samtools.github.io/hts-specs/

Other useful tools/libs

• NCBI Genome Workbench

• svviz

• ViVar

• UpSetR | Shinny app

• Varapp

• SVanalyze

• MoMI-G - genome graph browser

• Samtools

• Bamtools

• Sambamba

• svtools

• mergevcf (incl. some examples)

• merging-sv-calls

• RTG-tools

• vgraph

• SVDB

• IGV

• SeqAn

• vg - tools for working with genome variation graphs

Formats / Parsers

• VCFv4.3
• SAMv1
• VEP
• PyVCF
• genomics-data-parser
• Pysam (supports SAM/BAM/VCF/BCF)
• cyvcf2
• vcf-validator
• vcf2db
• VCF to npy, pandas, hdf5 etc.

Other links

• NCBI's Overview of Structural Variation
• Genome Reference Consortium
• ENCODE/DAC Blacklisted Regions on hg19