Is it possible to create a plink format file from these illumina data?
Hi Biostar readers
This is my first post to Biostar. I received some genotyping files from Illumina, and I want to convert them to Plink files. I have never seen formats like these.
I have 2 files, one with the illumina annotation:
rsID chrom position rsID.remapped
rs4477212 1 82154 rs4477212
rs1856862 1 121042 rs1856862
rs9701779 1 565374 rs9701779
LIB00013397_M 1 566213 rs9701099
kgp7727307 1 569624 rs6594035
And the second one, which must be ordered by chromosome and position. At first look is like this:
SNP CHR POS B Allele Freq Log R Ratio
200003 9 139906359 0.0013 -0.2434
200050 2 220089685 0.9831 -0.0449
200070 U 0 0 -0.0966
200078 16 16286614 1 -0.0952
200087 16 16246164 1 0.1238
Is there any option to transform them to plink format or any software which can reads the files?
I would appreciate any suggestions.
Thank you
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With the second file you can determine CNVs. Check software like PennCNV. Because the BAF and LRR are processed intensity values, I think you will not be able to determine SNPs out of it.
Thanks for your answer Jimbou