Conversion to vcf format for quality filtered SNPs

Question

[GR]

Hi All,

I am new to vcf format and SNP datasets. I have a very quick question. I have data as below:

1    1960    T    T    T    T    T    C    T    C    T    T    T    C    T    T    T    T    T    T    T    T    T
1    1961    A    T    A    A    A    A    A    A   T    T    T    A    T    T    T    T    T    T    T    T    T

• col1- chr
• col2- position
• col3- ref base
• col4 to col23- base calls from multiple individuals (same species).

This SNP data is already quality filtered. I was wondering if it will be possible to convert this to the vcf format?

Thanks,
RT

Answer 1

[Devon Ryan]

Yes, it's possible.

[GR]

Thanks Devon. vcf format has 8 fixed, mandatory columns. What should I do for col 6 QUAL, 7 FILTER and 8 INFO? I don't have data for these. Only I know that the SNP data has already passed the qual filters.

If you could give me some hints how to do that then that would be very helpful. Any example format will be of great help.

[Devon Ryan]

QUAL can be any numeric value, since you're not going to actually use it for anything. FILTER is PASS, since you said you already filtered. INFO can just be the allele frequency, since, again, your not going to use this field for anything. Just make the header match whatever you put in INFO.