This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to Convert Illumina reports to Vcf files?

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

snp
• 10,914 views • link
updated by Giulio Genovese • Giulio Genovese • written by vikrantvicky.1987 • 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

• 1 views • link
updated by finswimmer finswimmer • written by vikrantvicky.1987 • vikrantvicky.1987

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

• 0 views • link
written by jtftyl • jtftyl

2 answers

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

See previous discussion on converting to ped here:

And then ped to vcf:

• 1 views • link
written by igor igor

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.

• 1 views • link
written by Giulio Genovese • Giulio Genovese

Log in to answer this question.

More posts like this