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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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hmm file for custom designed array--illumina #22

Closed lirr-lichen closed 6 years ago

lirr-lichen commented 6 years ago

Hi Dr. Wang,

I want to use PennCNV to call CNV from a custom designed pig Illumian array ,this array were designed in 2017. My problem is that in the CNV calling step, I do not HMM file. Can I just use the hhall.hmm for no human species Illumina custom designed array?

Best, Lichen

kaichop commented 6 years ago

you can use hhall.hmm for this.

On Wed, Jan 10, 2018 at 8:48 PM, lirr-lichen notifications@github.com wrote:

Hi Dr. Wang,

I want to use PennCNV to call CNV from a custom designed pig Illumian array ,this array were designed in 2017. My problem is that in the CNV calling step, I do not HMM file. Can I just use the hhall.hmm for no human species Illumina custom designed array?

Best, Lichen

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lirr-lichen commented 6 years ago

Thank you for answering my question !

dtx282000 commented 4 years ago

Hi Dr. Wang,

I want to use PennCNV to call CNV from the 90K Axiom buffalo SNP array. My problem is that in the CNV calling step. Which HMM file is suitable for my CNV calling?

Best

kaichop commented 4 years ago

hhall.hmm can be used for all Illumina arrays. You just need to create a PFB file using compile_pfb.pl

On Fri, Aug 14, 2020 at 5:50 AM dtx282000 notifications@github.com wrote:

Hi Dr. Wang,

I want to use PennCNV to call CNV from the 90K Axiom buffalo SNP array. My problem is that in the CNV calling step. Which HMM file is suitable for my CNV calling?

Best

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/22#issuecomment-673993156, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OFZM34QI527W43GW3TSAUCGRANCNFSM4ELI2EWA .

dtx282000 commented 4 years ago

Hi Dr. Wang,

The 90K Axiom buffalo SNP array is not the Illumina array, which belong to the Affymetrix array. And the PFB file has been constructed using the compile_pfb.pl. Now, I would like to know if the affygw6.hmm can be used for all Affymetrix arrays. or any other suggestion?

Best

kaichop commented 4 years ago

You can try it. Also see an example paper https://pubmed.ncbi.nlm.nih.gov/27773354/ for analyzing Axiom array on human.

On Fri, Aug 14, 2020 at 11:05 PM dtx282000 notifications@github.com wrote:

Hi Dr. Wang,

The 90K Axiom buffalo SNP array is not the Illumina array, which belong to the Affymetrix array. And the PFB file has been constructed using the compile_pfb.pl. Now, I would like to know if the affygw6.hmm can be used for all Affymetrix arrays. or any other suggestion?

Best

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/22#issuecomment-674339521, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OFZQWBWXGCUMW2SJW3SAX3O7ANCNFSM4ELI2EWA .