ParseCNV2: CNV GWAS Tool

Parse Copy Number Variation from Array and Sequencing

Cite: Glessner JT, Li J, Liu Y, Khan M, Chang X, Sleiman PMA, Hakonarson H. ParseCNV2: efficient sequencing tool for copy number variation genome-wide association studies. Eur J Hum Genet. 2022 Nov 1. doi: 10.1038/s41431-022-01222-7. Epub ahead of print. PMID: 36316489.
Original: Glessner JT, Li J, Hakonarson H. ParseCNV integrative copy number variation association software with quality tracking. Nucleic Acids Res. 2013 Mar 1;41(5):e64. doi: 10.1093/nar/gks1346. Epub 2013 Jan 4. PMID: 23293001; PMCID: PMC3597648.

Test Commands Updated to include 2 options needed for test data and latest options -stat fisher -no_freq

Make sure compiles and Print Usage Message

perl ParseCNV2.pl

Specify a sequencing CNV call VCF, affected samples, and genome build

perl ParseCNV2.pl -i v4.3.vcf -c Cases_vcf.list -b hg19 -m 1 -stat fisher -no_freq

Specify an array CNV call text file, affected samples, and genome build

perl ParseCNV2.pl -i Cases.rawcnv -c Cases.list -b hg19 -stat fisher -no_freq

Specify an array CNV call text file, quantitative trait for samples, genome build, and batch to track

perl ParseCNV2.pl -i Cases.rawcnv -q Cases.qt -m 1 -d 2 -p 1 -b hg19 -batch ID_Category.txt -stat fisher -no_freq

Specify an array CNV call text file, perform quality control, plink format SNP genotype bed file, PennCNV detect_cnv log, affected samples, and genome build

perl ParseCNV2.pl -i Cases.rawcnv -qc -bfile plinkBed -log penncnv.log -c Cases.list2 -b hg19 -stat fisher -no_freq

Specify an array CNV call text file, affected samples, and genome build, covariates file, and statistic as logistic

perl ParseCNV2.pl -i Cases.rawcnv -c Cases.list -b hg19 -covar SamplesAgeSexRace.txt -stat logistic -no_freq

Update: ParseCNV2_6-28-22.pl is the last version of the original model of convert all inputs to rawcnv2 format
ParseCNV2.pl now has several upgrades including the new model of convert all inputs to vcf format and integrating Plink2 and RvTests

perl ParseCNV2.pl -i CNV_Calls[.vcf/.rawcnv] [-c Cases.txt/-q Samples_QuantitativeTrait.txt] [arguments]

Required arguments:

-i input[vcf/rawcnv/txt]
-c cases
-b build (if vcf can be inferred)

Optional arguments:

-o output
-covar covariates file
-stat statistic (fisher, logistic, or linear) or RvTests:
Single variant: score, wald, exact, dominantExact, famLRT, famScore, famGrammarGamma, firth
Burden: cmc, zeggini, mb, fp, exactCMC, cmcWald, rarecover, cmat, famcmc, famzeggini
Variable threshold: price, analytic, famAnalytic
Kernel: skat, skato, kbac, famSkat
Meta-Analysis: score, dominant, recessive, cov, bolt, boltCov
-no_freq No CNV frequency filtering, default is rare (minor allele frequency <0.01) recurrent (minor allele count > 2)
-p merge p variation
-d merge distance
-t transmission disequilibrium test
-m max p inclusion
-bfile plink bed file of SNP genotypes
-qc quality control upfront
-log penncnv log
-q quantitative trait
-b batch
-h help