Canary output subsequent analysis

Question

[Myosotis1979]

Dear all I have generated a gvar file using Canary algorithm to call copy number polymorphisms. Then, I generated a summary file of it using PLINK. Here a subset of the file:

        NAME        FIELD        VALUE
        CNP3          CHR            1
        CNP3           BP       777800
        CNP3          CNV           no
        CNP3      ALLELIC           no
        CNP3       GCOUNT           42
        CNP3      INTEGER            Y
        CNP3            A            1
        CNP3          [2]            1
        CNP3          0/0         59:0
        CNP3      AA/null         42:0
        CNP4          CHR            1
        CNP4           BP      1640120
        CNP4          CNV          yes
        CNP4      ALLELIC           no
        CNP4       GCOUNT           43
        CNP4      INTEGER            Y
        CNP4            A            1
        CNP4          [1]      0.02326
        CNP4          [2]       0.9767
        CNP4          0/0         58:0
        CNP4       A/null          1:0
        CNP4      AA/null         42:0
        CNP6          CHR            1
        CNP6           BP      8108521
        CNP6          CNV           no
        CNP6      ALLELIC           no
        CNP6       GCOUNT           41
        CNP6      INTEGER            Y
        CNP6            A            1
        CNP6          [2]            1
        CNP6          0/0         60:0
        CNP6      AA/null         41:0

I have many questions: - How to distinguish which are polymorphic CP ? - How to convert this file into an input file to STRUCTURE (population stratification software) as well as for the PCA analysis? - Should I use all these CNP for linkage desequilibrium analysis or should I filter to those which have "yes" value in this file ? Your help is valuable as I spent a lot of time searching for a tutorial in vain. Many thanks

[Kevin Blighe]

Hello, in which format was your original ata? - CEL files? Which platfom? - Affymetrix SNP 6.0?

[Myosotis1979]

Hello, CEL files for Affymetrix 6.0 plateforme

[Kevin Blighe]

okay, and how did you perform Canary? - using Affymetrix Genotyping Console?

[Myosotis1979]

I performed Canary according to the BirdSuite pipeline

[Kevin Blighe]

...and what is the input format required for STRUCTURE? You know that you can do PCA and MDS in PLINK, too?

[Kevin Blighe]

You already have your data in PLINK PED or BED format, right?