Getting a .vcf file from a Illumina SNPChip results (.bsc file)

Question

[valopes]

Hi all.

I am struggling to get a .vcf file from an Illumina SNPChip results (.bsc file). I opened the .bsc file using GenomeStudio software and exported results in PLINK format, using Plink plugin...

Like this, I've got .ped and .map files (but not .bed, .bim or .fam files). Now I am trying to use PLINK/SEQ to reach the vcf file I need, but with no success.

Could someone help me with this problem... I've already tried so many things.

Thanks in advance!

Answer 1

[Kevin Blighe]

Just use plink's --recode vcf function, introduced in plink2, I believe. Further information: https://www.cog-genomics.org/plink/1.9/data#recode

In addition, if you want to convert the plain text format (PED) to binary (BED), then use the --make-bed option: https://www.cog-genomics.org/plink/1.9/data#make_bed

If this produces an 'empty' VCF with minimal information, then you can add further information with BCFtools plugins: A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?

Kevin

[valopes]

Hi Kevin!

Thank you! Actually, a did quite the opposite. I first generate.bed, .bim and .fam:

plink --file text_fileset --make-bed --out binary_fileset

and then, from .bed to .vcf

plink --bfile binary_fileset --recode vcf --out new_vcf

It looks it worked. .vcf file is not empty, however, when I try to open it using IGV, it doesn't open.

Now I need to figure out next step.

Thanks

[Kevin Blighe]

What is the error that IGV gives?

[valopes]

It does not open the file... but I could open the same .vcf on Tassel.

[Kevin Blighe]

Your VCF must be failing the validation for VCF format specification that IGV performs. If you try to bgzip and then tab-index the VCF, are any errors returned? Can you paste the VCF header and a few variants?

[sam.far.7]

Hi Kevin Blighe, I have the same problem here, I've extracted the final GeniomeStudio report in a .txt format, now I need to convert it to .vcf to be able to use plink further. no luck just by mv .txt to .vcf getting the error of no header when I tried to convert to plink files. Can you please advise me on this? Best, Sami

[Kevin Blighe]

Hey Sami, can you look inside the file at its contents? How do they appear the first few lines?

[sam.far.7]

The head looks like this:

[Header]
GSGT Version    2.0.5
Processing Date 10/19/2020 2:43 PM
Content     GSA-24v1-0_A1_avera_20170513f_stranded.bpm
Num SNPs    697486
Total SNPs  697486
Num Samples 500
Total Samples   500
[Data]
SNP Name    Sample ID   Allele1 - Top   Allele2 - Top   GC Score    X   Y   X Raw   Y Raw   B Allele Freq   Log R Ratio

[Kevin Blighe]

Hmm, that is not the VCF format. Is there a VCF export option in GenomeStudio? If I remember correctly, there should be a specific option for it.

[sam.far.7]

Hi Kevin, I was able to find the PLINK format extraction. Thanks for your help.

Best, Sami