Is it possible to create a plink format file from these illumina data?
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7.5 years ago
cat_car • 0

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

plink illumina gwas • 1.8k views
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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.

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