Converting Illumina report files to input files for Imputation in FImpute, Beagle and Eagle


My apologies if this question has been answered before, but I have been searching to find an answer that fits my question for a while now.

I have report files from Illumina and I would like to prepare the files to a format that I can use for imputation in Beagle and Eagle. I wish to compare the results for both programs and also FImpute.

The files have the following columns:

Map files:

chip_key snp_name lab_snp_name chromosome position snp manuf_strand cust_strand

Genotype files:

dna_test_key snp_name allele1_ab allele2_ab gc_score x y

Sample files:

dna_test_key anim_key parent_verified sample_id loci_cnt snp_cnt

Thank you in advance.





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