Question: Getting a .vcf file from a Illumina SNPChip results (.bsc file)
0
gravatar for valopes
2.2 years ago by
valopes30
valopes30 wrote:

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!

snp • 1.1k views
ADD COMMENTlink modified 2.2 years ago by Kevin Blighe61k • written 2.2 years ago by valopes30
0
gravatar for Kevin Blighe
2.2 years ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Kevin Blighe61k

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

ADD REPLYlink written 2.2 years ago by valopes30

What is the error that IGV gives?

ADD REPLYlink written 2.2 years ago by Kevin Blighe61k

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

ADD REPLYlink written 2.2 years ago by valopes30

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?

ADD REPLYlink written 2.2 years ago by Kevin Blighe61k
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