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Old 09-05-2012, 08:51 AM   #1
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Default Software for Illumina Omni SNP array?

Is there any software available at the moment for looking at data from illumina Omni arrays?
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Old 09-05-2012, 07:41 PM   #2
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crlmm supposedly can also call genotypes for Omni arrays. However, I tried their 1.6.2 and found genotyping errors in the chrX SNPs. Not sure if it is fixed in their latest version though.
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Old 08-01-2013, 05:30 AM   #3
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Default Illumina Omni CNV analysis


I have problem in analyzing CNV for one sample. In this sample LRR profile around(0.0) remains FLAT, though not BAF profile (0.6 & 0.4) and as per ASCAT (software I am using) there is no copy number change.
Has any of you come across a similar issue?
Was wondering if it possible to analyze data with low cellularity and is more a technical issue of the software I am using.
Any pointers would be very helpful.

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