Csv. To VCF. File convert
0
2
Entering edit mode
23 months ago

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 • 2.8k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

A simple python script would do the job.

ADD REPLY
0
Entering edit mode

Can you elaborate? How can a "simple python script" add information that isn't there to get a VCF dataset from a CSV dataset without heavy customizations?

ADD REPLY
0
Entering edit mode

This is not a csv. Of course you need to have all the information required for format conversion including the Genome sequence.

ADD REPLY
0
Entering edit mode

So what's the reasoning behind your previous back-handed comment that ignores all the crucial aspects of the problem? A "simple" python script could do the job if the job were well defined, all data points required were available in an easy to parse format and OP knew how to code in Python and write VCF format output.

I mean, why even add a comment that adds no value to the post?

ADD REPLY

Login before adding your answer.

Traffic: 1146 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6