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  • Software for Illumina Omni SNP array?

    Is there any software available at the moment for looking at data from illumina Omni arrays?

  • #2
    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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    • #3
      Illumina Omni CNV analysis

      Hi,

      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.

      Best
      Shruti

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