From read counts to genotypes, or even better, a vcf

Question

[Joanna.ilska]

Hi all,

I am fairly new to dealing with sequence data and have come across a problem which I am not entirely sure how to bite.

I need to do an imputation from variants called using low coverage to variants called using high coverage data. Both my target and reference panels are in table format (output of GATK 3.5 VariantsToTable), as read counts. The read counts were edited using a custom script, so I can't just go back to the vcf file from which they were originally called for the imputation.

Does anyone know how I can address this? Is there any way of converting table to vcf, supplying the new edited read counts? Alternatively, what is the most efficient way of converting the read counts to genotypes?

Thank you in advance!

[Kevin Blighe]

Can you paste a sample of what exactly you've got?