Question: Csv. To VCF. File convert
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gravatar for kevinbruckner97
7 weeks ago by
kevinbruckner970 wrote:

Hello Biostars, It's my first post in here. I need to know, is there some way to convert .csv file, that I downloaded from TellmeGen , to .vcf file format? It looks pretty same, but .csv is comma-separated, and there is no header lines in it. How can I make it looks like classical vcf file? Thank you for your answers! The file looks like this:

No. 1 10:43597877_CNV_RET_e3_20 Chromosome 10 Position 43597877 Genotype GG.
gene • 211 views
ADD COMMENTlink modified 7 weeks ago by RamRS28k • written 7 weeks ago by kevinbruckner970

I'm guessing you opened the CSV file in Excel and copy pasted the content here, because the content does not look like CSV - there are no commas.

The information content in that record is too low for it to be transformed into a well formed VCF file. Why are you looking to get a VCF anyway?

ADD REPLYlink written 7 weeks ago by RamRS28k

Yes, that is not a CSV, seems to be regular text, please clarify.

To generate a VCF you will need to parse the file and the Genome sequence used to do the variant call or array design, use the VCF format spec definition to create a translator.

ADD REPLYlink written 7 weeks ago by JC11k
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