Hi all,

    We are using two methods to identify SNPs. One is based on resequencing
the genome and aligning the reads to the sequenced genome to identify SNPs
(data available for 44 individuals). Another is based on  SNP array with
selected loci (30000 loci, 870 individuals). I want to compare the results
from the resequencing based minor allele frequency and Array based minor
allele frequency. What statistical test should I use?

My table looks like



Chromosome           position               Major/minor
Resequencing                 SNP array


chromosome 1         198432                 C/T
75/13                             1460/280
chromosome 1         14282752             A/G
69/19                             1380/360
chromosome 1          595434                T/G
83/5                               1680/60


I really appreciate any guidance.

Thanks
Scott

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