Extracting REF and ALT from VCF

[kasthuri]

vcf's are naturally text files. If yours isn't, it's just compressed, so uncompress it.

Thank you swbarnes2. I found VariantsToTable in GATK does exactly what I wanted.

[swbarnes2]

vcf's are naturally text files. If yours isn't, it's just compressed, so uncompress it.

[kasthuri]

Thank you, id0. It works and I get the genotypes. But I don't get other information from the FORMAT fields. I know I can use --extract-FORMAT-info separately and 'paste' these two lists, but I would be more comfortable if I can get the genotypes as well as the format fields information at the same time. Anyway, I thank you for the solution.

Also, I will be just happy with the ALT entries instead of actual variants. Is it possible to get that?

Thanks
-K.

[kasthuri]

I think vcf-to-tab does exactly that:
vcf-to-tab < file.vcf

Thank you, id0. It works and I get the genotypes. But I don't get other information from the FORMAT fields. I know I can use --extract-FORMAT-info separately and 'paste' these two lists, but I would be more comfortable if I can get the genotypes as well as the format fields information at the same time. Anyway, I thank you for the solution.

[id0]

I think vcf-to-tab does exactly that:
vcf-to-tab < file.vcf

[kasthuri]

This may be a simple question.

I am trying to extract CHR, POS, REF and ALT and other info from a VCF file to a txt file using vcftools. Can somebody point me how to get REF and ALT? I don't get this information but everything else.

Thanks
-K.