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Hmm file for illumina cytoSNP 850K array #84
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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.
…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.
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Dear Developer, Which .hmm file should I use against Affymetrix Precision Medicine Research Array? |
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.
…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?
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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.
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