How to Convert Illumina reports to Vcf files?

Question

[vikrantvicky.1987]

Hi All,

I am new to CNV analysis and Vcf file conversion.

I have an Illumina text report and I am looking for a solution how can I convert them into a vcf file(with BAF and LRR) for copy number variation analysis by using bcftools/cnv

my input file looks like:

[Header]
GSGT Version 1.9.4
Processing Date 3/6/2014 10:39 AM
Content humancore-12v1-0_a.bpm
Num SNPs 298930
Total SNPs 298930
Num Samples 24
Total Samples 24
File 7 of 24
[Data]

Sample Index Sample ID Sample Name SNP Index SNP Name Chr Position GT Score GC Score Allele1 - AB Allele2 - AB Allele1 - Top Allele2 - Top Allele1 - Forward Allele2 - Forward Allele1 - Design Allele2 - Design Theta R X Raw Y Raw X Y B Allele Freq Log R Ratio SNP Aux SNP ILMN Strand Top Genomic Sequence Customer Strand

Thanks in Advance

Vikrant

[vikrantvicky.1987]

Hi Igor,

Thank you for the answer. I have already tried Plink to get vcf files by using above threads and generated vcf files.

Output given below:

##fileformat=VCFv4.2
##fileDate=20160806
##source=PLINKv1.90
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  7_BG01V
1   752566  rs3094315   T   .   .   .   PR  GT  0/0
1   752721  rs3131972   C   .   .   .   PR  GT  0/0
1   798959  rs11240777  G   .   .   .   PR  GT  0/0
1   838555  rs4970383   T   G   .   .   PR  GT  0/1
1   846808  rs4475691   T   C   .   .   PR  GT  0/1

But I need vcf file with BAF and LRR values in it for further analysis.
Do you have any idea how can I do that?

Thanks in advance.

Regards, Vikrant

[jtftyl]

Hello Vikrant:

I have the same situation. I received the Illumina text report. I was asked to convert into vcf. Did you use plink to convert the Illumina text report into PED then VCF? If so, how did it go?

Thanks Jenny

Answer 1

[igor]

You may have to convert to plink ped and then vcf.

See previous discussion on converting to ped here:

• Illumina genotyping report to Plink files
• Converting Illumina Raw Genotype Data Into Plink Ped Format
• Formatting Beadstudio Final Report Into Plink

And then ped to vcf:

• How To Convert .Ped To .Vcf File
• How To Convert Vcf File To Plink Ped Format?

Answer 2

[Giulio Genovese]

I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand.