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How can i get bovine50k HMM file for penncnv

How can i get HMM file and GCmodel file for penncncv, i m using bovineSnp50k chip data.

snp hmm file cnv analysis

You have to create them yourself. Here is the guidance from the PennCNV FAQ:

How to process arrays other than HumanHap550?

The PennCNV was originally developed for Illumina HumanHap550 array (in the Genome Research paper) but has been extended to other arrays. In PennCNV, the hhall.hg18.pfb, hhall.hmm and hhall.hg18.gcmodel files have been provided in the lib/ folder. They can be used to process arrays such as HumanHap300, HumanHap550, HumanHap650, HumanHap1M, HumanCNV370, Human610, Human1. For Affymetrix arrays, the PennCNV-Affy package contains library files for commonly used marker sets. In a nut shell, PennCNV can process an array if markers for this array are annotated in the PFB file.

For other Illumina&Affymetrix SNP arrays (for example, the Illumina Omni 2.5M array, or the Affy cytogenetics array), the user needs to compile your own PFB file that specifies the chromosome coordinates and PFB value for each marker in the array. Use the compile_pfb.pl program included in the PennCNV package for doing that.

[source: http://penncnv.openbioinformatics.org/en/latest/misc/faq/]

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