csv into genome browser

Question

[H.Hasani]

Dear Biostars,

this might be a simple question, I'm looking for a way to convert my csv files into an acceptable format, so that I can visualize my data in genome browser. Moreover, my csv files are the simplified version of annotated output, therefore, I hope I can visualize the AA change, Consequence, & additional flag (e.g. sample ID).

Any advise would be highly appreciated

Edit: I realized that my question is very vague. Maybe the first is first! Is there anyway to convert csv files into vcf ?

Thanks!

[Irsan]

A csv file can contain anything. What kind of data are you talking about? single nucleotide variants/insertions & deletions, copy number, chipseq, methylation?

[H.Hasani]

The csv file contains only annotated SNVs e.g. Gene, CHROM, POS, ID, AA, Consequence, Flag

[Irsan]

Then make sure you have a VCF file, because that is the standard format for SNVs. IGV can import and visualize VCFs.

[H.Hasani]

That was the reason for asking the original question! I could not find a way to convert csv to vcf particularly.

[GenoMax]

I realized that my question is very vague. Maybe the first is first! Is there anyway to convert csv files into vcf ?

You realized this after 4 months and chose to edit the original post or is there a new question in there somewhere?

I see that you added an answer below as well :-)

[H.Hasani]

No! The realization came right after receiving the first comments. To keep the original question intact I added lines after the "edit". This way people who answered and those who stop by, as yourself, still can follow this thread.

Few days ago, I added the answer that I learnt and back then did not know about. I thought it might be of interest to someone else.

By the way, accepting my own answer did not give me extra credit :)

Answer 1

[Jean-Karim Heriche]

You could try genoverse, I think it can read CSV files.

[H.Hasani]

Looks interesting, I'll try it. Thanks!

Answer 2

[H.Hasani]

For those who were looking for similar approach, I found that Personal Genome SNP format is the closest thing to my needs, as the AA change will be automatically linked to each SNP once it is correctly uploaded.