Hmm file for illumina cytoSNP 850K array

[Sneha-bioinfo]

I'm working on cancer samples run on illumina cytoSNP 850K array ( probes designed on GRCh38). I am trying to use PennCNV to detect the copy number variation from the data. Which hmm file would be appropriate for this? I couldn't find any hmm file trained on GRCh38 in the site.

[kaichop]

For Illumina arrays, you can just use hall.hmm. It is not related to genome coordinate. Also make sure you make PFB file using compile_pfb.pl and using the signal files with GRCh38 coordinate.

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On Sat, May 14, 2022 at 1:11 PM Sneha Das ***@***.***> wrote: I'm working on cancer samples run on illumina cytoSNP 850 array ( probes designed on GRCh38). I am trying to use PennCNV to detect the copy number variation from the data. Which hmm file would be appropriate for this? I couldn't find any hmm file trained on GRCh38 in the site. — Reply to this email directly, view it on GitHub <#84>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OCQ5B2L2VAY2EEXS6DVJ7NE3ANCNFSM5V52SYHQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[chopraamhk]

Dear Developer,

Which .hmm file should I use against Affymetrix Precision Medicine Research Array?

[kaichop]

This is Axiom array. You may want to read the paper below and follow the procedures there. - 20161024: Prof. George Kirov shared a recently published paper reporting the use of PennCNV on Affy Axiom arrays here <https://pubmed.ncbi.nlm.nih.gov/27773354/>. Detailed procedure for CNV calling is given in the supplementary materials.

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On Mon, May 23, 2022 at 9:57 PM Mehak Chopra ***@***.***> wrote: Dear Developer, Which .hmm file should I use against Affymetrix Precision Medicine Research Array? — Reply to this email directly, view it on GitHub <#84 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OGU7NT4SFZS5KGTOGTVLQZRFANCNFSM5V52SYHQ> . You are receiving this because you commented.Message ID: ***@***.***>