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PennCNV #
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Structured data

SNP array
Copy-number variation
Programming Language

SNP array 데이터에서 CNV를 탐지하는 프로그램

PennCNV implements a HMM that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone.

In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

PennCNV-Affy #

Data processing protocol for Genome-Wide Human SNP Array 6.0. It converts raw CEL files into a signal intensity file that contains Log R Ratio (LRR) and B Allele Frequency (BAF) vlaues.


  1. Generate genotyping calls from CEL file using Affymetrix Power Tools apt-probeset-genotype program
  2. Allele-specific signal extraction from CEL files using Affymetrix Power Tools apt-probeset-summarize
  3. Generate canonical genotype clustering file by
  4. LRR and BAF calculation by
  5. Split the signal file into individual files and running CNV calling

CNV calling #

Input file from

  1. PennCNV-Affy
  2. Illumina Report
  3. BeadStudio project file


Output example (rawcnv)

chr1:160659106-160915937      numsnp=79     length=256,832     state2,cn=1 gw6.Genomewide6 startsnp=CN_442866 endsnp=CN_442942
chr1:163703204-165581459      numsnp=645    length=1,878,256   state2,cn=1 gw6.Genomewide6 startsnp=CN_453837 endsnp=CN_439198
chr1:165901010-169387961      numsnp=1191   length=3,486,952   state2,cn=1 gw6.Genomewide6 startsnp=CN_440397 endsnp=CN_452581
chr1:169448874-169643388      numsnp=53     length=194,515     state2,cn=1 gw6.Genomewide6 startsnp=CN_452606 endsnp=CN_452661
chr1:169825272-171629811      numsnp=615    length=1,804,540   state2,cn=1 gw6.Genomewide6 startsnp=CN_453958 endsnp=CN_439314
chr2:7876421-8183989          numsnp=120    length=307,569     state2,cn=1 gw6.Genomewide6 startsnp=CN_202764 endsnp=CN_860524
chr2:54108877-55094559        numsnp=360    length=985,683     state2,cn=1 gw6.Genomewide6 startsnp=CN_846479 endsnp=CN_853178

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