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

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

plink illumina gwas • 1.8k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thanks for your answer Jimbou

ADD REPLY

Login before adding your answer.

Traffic: 1168 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6