This repository contains following scripts:

• processing whole-exome sequencing data
• construction of validation set based on multiple data
• choise of reference set and running CNV callers
• analysis of CNV calling tools perfomance

Datasets:

Exome data: The 1000 Genomes Project Phase 3 (samples)

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/exome_pull_down_targets/20130108.exome.targets.bed

Compared CNV calling tools:

• CANOES (Backenroth et al. Nucleic Acids Res, 2014)
• CLAMMS (Packer et al. Bioinformatics, 2015)
• cn.MOPS (Klambauer* et al, Nucleic Acids Res*, 2012)
• CNVkit (Talevich et al. PLOS Computational Biology, 2016)
• CODEX (Jiang et al. Nucleic Acids Res, 2015)
• CoNIFER (Krumm et al. Genome Research, 2012)
• CONTRA (Li et al. Bioinformatics, 2012)
• DeAnnCNV (Zhang et al. Nucleic Acids Res, 2015)
• EXCAVATOR2 (D'Aurizio et al. Nucleic Acids Res, 2016)
• exomeCopy (Samarakoon et al BMC Genomics, 2014)
• ExomeDepth (Plagnol et al. Bioinformatics, 2012)
• ExonDel (Guo et al. BMC Bioinformatics, 2014)
• FishingCNNV (Shi et al. Bioinformatics, 2013)
• HMZDelFinder (Gambin et al. Bioinformatics, 2017)
• PatternCNV (Wang et al. Bioinformatics, 2014)
• XHMM (Fromer et al. Am J Hum Genet, 2012)

CNV sets used to construct internal standard for NA12878 at exon level

• mccarroll2006 (McCarroll et al. Nature Genetics, 2006)

ftp://ftp.ebi.ac.uk/pub/databases/dgva/nstd20_McCarroll_et_al_2006/gvf/nstd20_McCarroll_et_al_2006.2015-11-02.GRCh37.Remapped.gvf

• conrad2006 (Conrad et al. Nature Genetics, 2006)

ftp://ftp.ebi.ac.uk/pub/databases/dgva/nstd17_Conrad_et_al_2006/gvf/nstd17_Conrad_et_al_2006.2015-11-02.GRCh37.Remapped.gvf

• wang (Wang et al. Genome Research, 2007)

ftp://ftp.ebi.ac.uk/pub/databases/dgva/nstd64_Wang_et_al_2007/gvf/nstd64_Wang_et_al_2007.2017-10-03.GRCh37.Remapped.gvf 

• pinto (Pinto et al. Human Molecular Genetics, 2007)

ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd55_Pinto_et_al_2007/gvf/estd55_Pinto_et_al_2007.2014-04-02.GRCh37.Remapped.gvf

• cooper (Cooper et al. Nature Genetics, 2008)

ftp://ftp.ebi.ac.uk/pub/databases/dgva/nstd14_Cooper_et_al_2008/gvf/nstd14_Cooper_et_al_2008.2015-11-02.GRCh37.Remapped.gvf

• mccarroll2008 ( McCarroll et al. Nature Genetics, 2008)

https://static-content.springer.com/esm/art%3A10.1038%2Fng.238/MediaObjects/41588_2008_BFng238_MOESM24_ESM.xls
https://static-content.springer.com/esm/art%3A10.1038%2Fng.238/MediaObjects/41588_2008_BFng238_MOESM25_ESM.xls

• hapmap (International HapMap 3 Consortium, et al. Nature, 2010)

ftp://ftp.ncbi.nlm.nih.gov/hapmap/cnv_data/hm3_cnv_submission.txt

• conrad2010 (Conrad et al. Nature, 2010)

https://static-content.springer.com/esm/art%3A10.1038%2Fnature08516/MediaObjects/41586_2010_BFnature08516_MOESM10_ESM.xls

• pilot (The 1000 Genomes Project Consortium Nature, 2010 Mills et al. Nature, 2011)

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/paper_data_sets/companion_papers/mapping_structural_variation/MasterValidation.Pilot2.all.leftmost.061510.txt 

• phase1 (The 1000 Genomes Project Consortium Nature, 2012)

ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd199_1000_Genomes_Consortium_Phase_1/gvf/estd199_1000_Genomes_Consortium_Phase_1.2013-06-27.GRCh37.Submitted.gvf

• lumpy (Layer et al. Genome Biology, 2014)

https://static-content.springer.com/esm/art%3A10.1186%2Fgb-2014-15-6-r84/MediaObjects/13059_2013_3363_MOESM4_ESM.zip

• phase3 (Sudmant et al. Nature, 2015)

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz

• pacbio (Pendleton et al. Nature Methods, 2015)

ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NA12878_PacBio_MtSinai/NA12878.sorted.vcf.gz

• metasv (Parikh et al. BMC Genomics, 2016)

ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/metasv_trio_validation/NA12878_svs.vcf.gz

• svclassify (Parikh et al. BMC Genomics, 2016)

ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Personalis_1000_Genomes_deduplicated_deletions.bed 

• Stringent CNV map of human genome (Zarrei et al. Nat Rev Genet, 2015)

https://static-content.springer.com/esm/art%3A10.1038%2Fnrg3871/MediaObjects/41576_2015_BFnrg3871_MOESM27_ESM.xls